Starting phenix.real_space_refine on Sun Apr 5 03:41:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9on5_70629/04_2026/9on5_70629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9on5_70629/04_2026/9on5_70629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9on5_70629/04_2026/9on5_70629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9on5_70629/04_2026/9on5_70629.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9on5_70629/04_2026/9on5_70629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9on5_70629/04_2026/9on5_70629.map" } resolution = 2.6 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 1 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: 6 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: "B" 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: "C" 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 1.63, per 1000 atoms: 0.21 Number of scatterers: 7791 At special positions: 0 Unit cell: (86.52, 89.816, 120.304, 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=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 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 125 " - pdb=" SG CYS C 176 " distance=2.02 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " 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 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG A 503 " - " ASN A 310 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG B 503 " - " ASN B 310 " " NAG C 501 " - " ASN C 133 " " NAG C 502 " - " ASN C 194 " " NAG C 503 " - " ASN C 310 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 232.2 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: 27 helices and 9 sheets defined 25.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 41 through 61 removed outlier: 3.916A pdb=" N TYR A 59 " --> pdb=" O TYR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 353 Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.631A pdb=" N ILE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 61 removed outlier: 3.916A pdb=" N TYR B 59 " --> pdb=" O TYR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 353 Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.631A pdb=" N ILE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 61 removed outlier: 3.916A pdb=" N TYR C 59 " --> pdb=" O TYR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 353 Processing helix chain 'C' and resid 354 through 363 removed outlier: 3.632A pdb=" N ILE C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 71 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 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 71 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 71 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 71 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 88 196 hydrogen bonds defined for protein. 516 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: 0.97 Time building geometry restraints manager: 0.72 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: 2418 1.34 - 1.46: 1935 1.46 - 1.58: 3579 1.58 - 1.70: 15 1.70 - 1.81: 45 Bond restraints: 7992 Sorted by residual: bond pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG C 503 " pdb=" O5 NAG C 503 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O5' ATP B 504 " pdb=" PA ATP B 504 " ideal model delta sigma weight residual 1.579 1.605 -0.026 1.10e-02 8.26e+03 5.43e+00 bond pdb=" O5' ATP A 504 " pdb=" PA ATP A 504 " ideal model delta sigma weight residual 1.579 1.604 -0.025 1.10e-02 8.26e+03 5.34e+00 ... (remaining 7987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 10478 1.37 - 2.74: 312 2.74 - 4.11: 52 4.11 - 5.48: 28 5.48 - 6.85: 8 Bond angle restraints: 10878 Sorted by residual: angle pdb=" PB ATP C 504 " pdb=" O3B ATP C 504 " pdb=" PG ATP C 504 " ideal model delta sigma weight residual 139.87 133.02 6.85 1.00e+00 1.00e+00 4.69e+01 angle pdb=" PB ATP B 504 " pdb=" O3B ATP B 504 " pdb=" PG ATP B 504 " ideal model delta sigma weight residual 139.87 133.02 6.85 1.00e+00 1.00e+00 4.69e+01 angle pdb=" PB ATP A 504 " pdb=" O3B ATP A 504 " pdb=" PG ATP A 504 " ideal model delta sigma weight residual 139.87 133.04 6.83 1.00e+00 1.00e+00 4.66e+01 angle pdb=" PA ATP B 504 " pdb=" O3A ATP B 504 " pdb=" PB ATP B 504 " ideal model delta sigma weight residual 136.83 131.12 5.71 1.00e+00 1.00e+00 3.27e+01 angle pdb=" PA ATP C 504 " pdb=" O3A ATP C 504 " pdb=" PB ATP C 504 " ideal model delta sigma weight residual 136.83 131.12 5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 10873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 4629 24.54 - 49.09: 171 49.09 - 73.63: 66 73.63 - 98.17: 3 98.17 - 122.72: 9 Dihedral angle restraints: 4878 sinusoidal: 2097 harmonic: 2781 Sorted by residual: dihedral pdb=" C2 NAG A 503 " pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " pdb=" C5 NAG A 503 " ideal model delta sinusoidal sigma weight residual -62.96 59.76 -122.72 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C2 NAG C 503 " pdb=" C1 NAG C 503 " pdb=" O5 NAG C 503 " pdb=" C5 NAG C 503 " ideal model delta sinusoidal sigma weight residual -62.96 59.76 -122.72 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C2 NAG B 503 " pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " pdb=" C5 NAG B 503 " ideal model delta sinusoidal sigma weight residual -62.96 59.73 -122.69 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 4875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 740 0.034 - 0.067: 311 0.067 - 0.101: 113 0.101 - 0.134: 63 0.134 - 0.168: 12 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 194 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 194 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 194 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 1236 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 74 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO C 74 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 73 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO B 74 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " -0.022 5.00e-02 4.00e+02 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1133 2.76 - 3.30: 7006 3.30 - 3.83: 12806 3.83 - 4.37: 15316 4.37 - 4.90: 26614 Nonbonded interactions: 62875 Sorted by model distance: nonbonded pdb=" OE1 GLU B 96 " pdb=" OH TYR C 306 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 306 " pdb=" OE1 GLU C 96 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU A 96 " pdb=" OH TYR B 306 " model vdw 2.242 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.264 3.040 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.265 3.040 ... (remaining 62870 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: 0.03 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: 3.110 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.005 0.073 8016 Z= 0.214 Angle : 0.610 6.852 10935 Z= 0.353 Chirality : 0.048 0.168 1239 Planarity : 0.004 0.041 1344 Dihedral : 15.009 122.716 3063 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.81 % Allowed : 6.14 % Favored : 92.06 % 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 (0.27), residues: 963 helix: -0.21 (0.35), residues: 219 sheet: 0.74 (0.27), residues: 333 loop : -0.46 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.015 0.002 TYR B 222 PHE 0.008 0.001 PHE A 239 TRP 0.010 0.001 TRP C 268 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7992) covalent geometry : angle 0.60348 (10878) SS BOND : bond 0.00379 ( 15) SS BOND : angle 1.16095 ( 30) hydrogen bonds : bond 0.18309 ( 196) hydrogen bonds : angle 6.01430 ( 516) link_NAG-ASN : bond 0.00467 ( 9) link_NAG-ASN : angle 1.55576 ( 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 256 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8702 (tttp) cc_final: 0.8446 (tttt) REVERT: A 94 ASP cc_start: 0.7745 (p0) cc_final: 0.7521 (p0) REVERT: A 96 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6768 (tm-30) REVERT: A 127 GLU cc_start: 0.8177 (tp30) cc_final: 0.7710 (tp30) REVERT: A 220 ASP cc_start: 0.8049 (p0) cc_final: 0.7779 (p0) REVERT: A 344 ASN cc_start: 0.8319 (m-40) cc_final: 0.8055 (m110) REVERT: B 96 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6611 (tm-30) REVERT: B 97 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 280 ASN cc_start: 0.8044 (m-40) cc_final: 0.7829 (m-40) REVERT: B 289 ASP cc_start: 0.7528 (t0) cc_final: 0.7321 (t0) REVERT: B 343 ILE cc_start: 0.8608 (mp) cc_final: 0.8226 (tt) REVERT: B 344 ASN cc_start: 0.8170 (m-40) cc_final: 0.7962 (m110) REVERT: B 354 VAL cc_start: 0.8427 (p) cc_final: 0.8201 (t) REVERT: C 56 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: C 91 LYS cc_start: 0.8675 (tttp) cc_final: 0.8357 (tttp) REVERT: C 96 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6587 (tm-30) REVERT: C 97 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7897 (mt-10) REVERT: C 220 ASP cc_start: 0.8096 (p0) cc_final: 0.7836 (p0) REVERT: C 258 LYS cc_start: 0.8025 (tppt) cc_final: 0.7809 (tppt) outliers start: 15 outliers final: 7 residues processed: 254 average time/residue: 0.5153 time to fit residues: 138.5947 Evaluate side-chains 216 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 122 GLN A 280 ASN B 64 GLN B 122 GLN C 64 GLN C 204 HIS C 344 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.130549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116318 restraints weight = 10997.378| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.06 r_work: 0.3433 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8016 Z= 0.186 Angle : 0.607 9.013 10935 Z= 0.308 Chirality : 0.050 0.200 1239 Planarity : 0.005 0.040 1344 Dihedral : 14.794 106.849 1351 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.89 % Allowed : 14.20 % Favored : 82.91 % 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: -0.18 (0.27), residues: 963 helix: -0.53 (0.34), residues: 240 sheet: 0.85 (0.28), residues: 333 loop : -0.60 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.017 0.002 TYR A 98 PHE 0.009 0.001 PHE C 252 TRP 0.013 0.001 TRP B 268 HIS 0.003 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7992) covalent geometry : angle 0.59502 (10878) SS BOND : bond 0.00375 ( 15) SS BOND : angle 1.18717 ( 30) hydrogen bonds : bond 0.04871 ( 196) hydrogen bonds : angle 5.01987 ( 516) link_NAG-ASN : bond 0.00429 ( 9) link_NAG-ASN : angle 2.19914 ( 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 236 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6700 (tm-30) REVERT: A 127 GLU cc_start: 0.8201 (tp30) cc_final: 0.7997 (tp30) REVERT: A 179 GLU cc_start: 0.7673 (tt0) cc_final: 0.7378 (tt0) REVERT: A 220 ASP cc_start: 0.8196 (p0) cc_final: 0.7910 (p0) REVERT: A 273 ASP cc_start: 0.8597 (m-30) cc_final: 0.8354 (m-30) REVERT: A 344 ASN cc_start: 0.8231 (m-40) cc_final: 0.7993 (m110) REVERT: B 94 ASP cc_start: 0.7355 (p0) cc_final: 0.7099 (p0) REVERT: B 96 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 97 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 289 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7302 (t0) REVERT: B 343 ILE cc_start: 0.8507 (mp) cc_final: 0.8102 (tt) REVERT: C 191 MET cc_start: 0.7804 (mpp) cc_final: 0.7450 (mtm) REVERT: C 211 SER cc_start: 0.8651 (p) cc_final: 0.8396 (m) REVERT: C 220 ASP cc_start: 0.8270 (p0) cc_final: 0.7959 (p0) outliers start: 24 outliers final: 10 residues processed: 226 average time/residue: 0.5019 time to fit residues: 120.3413 Evaluate side-chains 214 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 289 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 280 ASN B 122 GLN B 344 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 = 0.3734 r_free = 0.3734 target = 0.130668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116588 restraints weight = 10940.351| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.03 r_work: 0.3437 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8016 Z= 0.178 Angle : 0.600 9.192 10935 Z= 0.299 Chirality : 0.050 0.283 1239 Planarity : 0.005 0.039 1344 Dihedral : 14.527 103.731 1349 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.25 % Allowed : 15.64 % Favored : 81.11 % 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: -0.16 (0.27), residues: 963 helix: -0.53 (0.34), residues: 240 sheet: 0.84 (0.28), residues: 333 loop : -0.56 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.015 0.001 TYR A 98 PHE 0.009 0.001 PHE B 239 TRP 0.015 0.001 TRP A 268 HIS 0.003 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 7992) covalent geometry : angle 0.58873 (10878) SS BOND : bond 0.00365 ( 15) SS BOND : angle 1.12352 ( 30) hydrogen bonds : bond 0.04283 ( 196) hydrogen bonds : angle 4.84014 ( 516) link_NAG-ASN : bond 0.00661 ( 9) link_NAG-ASN : angle 2.21362 ( 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 238 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8372 (tttp) REVERT: A 96 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 127 GLU cc_start: 0.8122 (tp30) cc_final: 0.7710 (tp30) REVERT: A 201 ASN cc_start: 0.8652 (t0) cc_final: 0.8447 (t0) REVERT: A 220 ASP cc_start: 0.8206 (p0) cc_final: 0.7927 (p0) REVERT: A 224 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8250 (mtpp) REVERT: A 273 ASP cc_start: 0.8604 (m-30) cc_final: 0.8369 (m-30) REVERT: A 344 ASN cc_start: 0.8230 (m-40) cc_final: 0.7988 (m110) REVERT: B 94 ASP cc_start: 0.7349 (p0) cc_final: 0.7125 (p0) REVERT: B 289 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7304 (t0) REVERT: B 343 ILE cc_start: 0.8504 (mp) cc_final: 0.8096 (tt) REVERT: C 96 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6744 (tm-30) REVERT: C 191 MET cc_start: 0.7781 (mpp) cc_final: 0.7454 (mpp) REVERT: C 211 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8401 (m) REVERT: C 220 ASP cc_start: 0.8300 (p0) cc_final: 0.8043 (p0) REVERT: C 224 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8206 (mtpp) outliers start: 27 outliers final: 14 residues processed: 226 average time/residue: 0.5036 time to fit residues: 120.8217 Evaluate side-chains 221 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 89 optimal weight: 0.0970 chunk 93 optimal weight: 0.5980 chunk 57 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 280 ASN B 122 GLN B 204 HIS B 344 ASN C 344 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117091 restraints weight = 11123.411| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.05 r_work: 0.3442 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1571 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= 0.136 Angle : 0.587 8.668 10935 Z= 0.287 Chirality : 0.049 0.287 1239 Planarity : 0.004 0.037 1344 Dihedral : 14.176 99.853 1349 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.73 % Allowed : 15.88 % Favored : 80.39 % 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 (0.27), residues: 963 helix: -0.26 (0.35), residues: 222 sheet: 0.80 (0.27), residues: 339 loop : -0.38 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.014 0.001 TYR A 98 PHE 0.007 0.001 PHE A 239 TRP 0.013 0.001 TRP A 268 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7992) covalent geometry : angle 0.57844 (10878) SS BOND : bond 0.00307 ( 15) SS BOND : angle 0.94973 ( 30) hydrogen bonds : bond 0.03710 ( 196) hydrogen bonds : angle 4.75173 ( 516) link_NAG-ASN : bond 0.00600 ( 9) link_NAG-ASN : angle 1.97695 ( 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 240 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.8329 (m) cc_final: 0.8064 (p) REVERT: A 81 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8389 (tttp) REVERT: A 96 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6718 (tm-30) REVERT: A 127 GLU cc_start: 0.8127 (tp30) cc_final: 0.7899 (tp30) REVERT: A 220 ASP cc_start: 0.8221 (p0) cc_final: 0.7947 (p0) REVERT: A 224 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8254 (mtpp) REVERT: A 273 ASP cc_start: 0.8603 (m-30) cc_final: 0.8367 (m-30) REVERT: A 344 ASN cc_start: 0.8188 (m-40) cc_final: 0.7968 (m110) REVERT: B 56 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.7037 (t80) REVERT: B 191 MET cc_start: 0.7981 (mtm) cc_final: 0.7699 (mtm) REVERT: B 211 SER cc_start: 0.8560 (p) cc_final: 0.8313 (m) REVERT: B 289 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7257 (t0) REVERT: B 343 ILE cc_start: 0.8449 (mp) cc_final: 0.8035 (tt) REVERT: C 96 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6751 (tm-30) REVERT: C 191 MET cc_start: 0.7833 (mpp) cc_final: 0.7299 (mpp) REVERT: C 211 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8381 (m) REVERT: C 220 ASP cc_start: 0.8296 (p0) cc_final: 0.8071 (p0) outliers start: 31 outliers final: 14 residues processed: 228 average time/residue: 0.5046 time to fit residues: 121.8064 Evaluate side-chains 223 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 280 ASN B 122 GLN B 204 HIS B 344 ASN C 204 HIS C 344 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116400 restraints weight = 11185.133| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.05 r_work: 0.3438 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8016 Z= 0.185 Angle : 0.619 10.434 10935 Z= 0.303 Chirality : 0.050 0.262 1239 Planarity : 0.004 0.037 1344 Dihedral : 13.895 96.570 1348 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.85 % Allowed : 16.00 % Favored : 80.14 % 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: -0.02 (0.27), residues: 963 helix: -0.38 (0.35), residues: 222 sheet: 0.81 (0.27), residues: 339 loop : -0.40 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 302 TYR 0.014 0.001 TYR C 222 PHE 0.009 0.001 PHE B 239 TRP 0.011 0.001 TRP A 268 HIS 0.003 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7992) covalent geometry : angle 0.60866 (10878) SS BOND : bond 0.00384 ( 15) SS BOND : angle 1.15743 ( 30) hydrogen bonds : bond 0.04025 ( 196) hydrogen bonds : angle 4.92826 ( 516) link_NAG-ASN : bond 0.00527 ( 9) link_NAG-ASN : angle 2.05551 ( 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 242 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8468 (mtpt) REVERT: A 70 SER cc_start: 0.8262 (m) cc_final: 0.8023 (p) REVERT: A 81 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8447 (tttp) REVERT: A 96 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6694 (tm-30) REVERT: A 220 ASP cc_start: 0.8219 (p0) cc_final: 0.7918 (p0) REVERT: A 254 GLU cc_start: 0.7739 (mp0) cc_final: 0.7520 (mp0) REVERT: A 273 ASP cc_start: 0.8621 (m-30) cc_final: 0.8368 (m-30) REVERT: A 344 ASN cc_start: 0.8193 (m-40) cc_final: 0.7986 (m110) REVERT: B 56 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.7034 (t80) REVERT: B 191 MET cc_start: 0.7994 (mtm) cc_final: 0.7723 (mtm) REVERT: B 211 SER cc_start: 0.8521 (p) cc_final: 0.8268 (m) REVERT: B 224 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8334 (mtpp) REVERT: B 289 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7312 (t0) REVERT: B 343 ILE cc_start: 0.8456 (mp) cc_final: 0.8059 (tt) REVERT: C 87 THR cc_start: 0.8717 (p) cc_final: 0.8459 (m) REVERT: C 96 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6706 (tm-30) REVERT: C 191 MET cc_start: 0.7827 (mpp) cc_final: 0.7316 (mpp) REVERT: C 211 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8390 (m) REVERT: C 220 ASP cc_start: 0.8333 (p0) cc_final: 0.8127 (p0) outliers start: 32 outliers final: 18 residues processed: 228 average time/residue: 0.5178 time to fit residues: 125.0427 Evaluate side-chains 231 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 63 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 6 optimal weight: 0.0030 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 280 ASN B 122 GLN B 204 HIS B 344 ASN C 344 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117796 restraints weight = 11095.852| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.04 r_work: 0.3457 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1795 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= 0.115 Angle : 0.597 9.440 10935 Z= 0.287 Chirality : 0.049 0.240 1239 Planarity : 0.004 0.036 1344 Dihedral : 13.245 92.943 1348 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.37 % Allowed : 17.57 % Favored : 79.06 % 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: 0.01 (0.27), residues: 963 helix: -0.31 (0.35), residues: 222 sheet: 0.76 (0.27), residues: 339 loop : -0.34 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 286 TYR 0.014 0.001 TYR C 98 PHE 0.007 0.001 PHE B 56 TRP 0.011 0.001 TRP A 268 HIS 0.001 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7992) covalent geometry : angle 0.58777 (10878) SS BOND : bond 0.00279 ( 15) SS BOND : angle 0.88921 ( 30) hydrogen bonds : bond 0.03425 ( 196) hydrogen bonds : angle 4.78824 ( 516) link_NAG-ASN : bond 0.00540 ( 9) link_NAG-ASN : angle 2.07944 ( 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: 28 poor density : 209 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8447 (mtpt) REVERT: A 96 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6705 (tm-30) REVERT: A 220 ASP cc_start: 0.8215 (p0) cc_final: 0.7945 (p0) REVERT: A 254 GLU cc_start: 0.7737 (mp0) cc_final: 0.7481 (mp0) REVERT: A 273 ASP cc_start: 0.8592 (m-30) cc_final: 0.8359 (m-30) REVERT: A 344 ASN cc_start: 0.8139 (m-40) cc_final: 0.7936 (m110) REVERT: B 56 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6939 (t80) REVERT: B 71 GLU cc_start: 0.7002 (tt0) cc_final: 0.6798 (tt0) REVERT: B 191 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7710 (mtm) REVERT: B 211 SER cc_start: 0.8521 (p) cc_final: 0.8268 (m) REVERT: B 224 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8309 (mtpp) REVERT: B 289 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7252 (t0) REVERT: B 343 ILE cc_start: 0.8400 (mp) cc_final: 0.8000 (tt) REVERT: C 96 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6778 (tm-30) REVERT: C 211 SER cc_start: 0.8622 (p) cc_final: 0.8372 (m) outliers start: 28 outliers final: 13 residues processed: 224 average time/residue: 0.5188 time to fit residues: 123.2592 Evaluate side-chains 226 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 0.0040 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 A 280 ASN B 122 GLN B 204 HIS B 344 ASN C 152 ASN C 204 HIS C 344 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116825 restraints weight = 11045.583| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.03 r_work: 0.3443 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8016 Z= 0.177 Angle : 0.629 9.680 10935 Z= 0.303 Chirality : 0.051 0.379 1239 Planarity : 0.004 0.035 1344 Dihedral : 12.857 89.533 1348 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.97 % Allowed : 17.21 % 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: 0.01 (0.27), residues: 963 helix: -0.34 (0.35), residues: 222 sheet: 0.80 (0.27), residues: 339 loop : -0.35 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.015 0.001 TYR A 98 PHE 0.008 0.001 PHE B 239 TRP 0.010 0.001 TRP B 268 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 7992) covalent geometry : angle 0.61559 (10878) SS BOND : bond 0.00360 ( 15) SS BOND : angle 1.12616 ( 30) hydrogen bonds : bond 0.03751 ( 196) hydrogen bonds : angle 4.87790 ( 516) link_NAG-ASN : bond 0.00658 ( 9) link_NAG-ASN : angle 2.49923 ( 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 246 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8449 (mtpt) REVERT: A 81 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8429 (tttp) REVERT: A 96 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6706 (tm-30) REVERT: A 220 ASP cc_start: 0.8224 (p0) cc_final: 0.7932 (p0) REVERT: A 273 ASP cc_start: 0.8601 (m-30) cc_final: 0.8358 (m-30) REVERT: A 344 ASN cc_start: 0.8160 (m-40) cc_final: 0.7953 (m110) REVERT: B 56 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6982 (t80) REVERT: B 71 GLU cc_start: 0.7030 (tt0) cc_final: 0.6827 (tt0) REVERT: B 211 SER cc_start: 0.8540 (p) cc_final: 0.8291 (m) REVERT: B 224 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8309 (mtpp) REVERT: B 289 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7284 (t0) REVERT: B 343 ILE cc_start: 0.8425 (mp) cc_final: 0.8033 (tt) REVERT: C 96 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6715 (tm-30) REVERT: C 191 MET cc_start: 0.7918 (mpp) cc_final: 0.7399 (mpp) REVERT: C 211 SER cc_start: 0.8653 (p) cc_final: 0.8395 (m) outliers start: 33 outliers final: 18 residues processed: 232 average time/residue: 0.4968 time to fit residues: 122.4100 Evaluate side-chains 233 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.0030 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 A 280 ASN B 122 GLN B 204 HIS B 344 ASN C 152 ASN C 204 HIS C 344 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117240 restraints weight = 11077.710| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.05 r_work: 0.3451 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1891 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= 0.141 Angle : 0.623 9.896 10935 Z= 0.299 Chirality : 0.050 0.364 1239 Planarity : 0.004 0.036 1344 Dihedral : 12.093 83.374 1348 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.49 % Allowed : 18.17 % Favored : 78.34 % 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: 0.02 (0.27), residues: 963 helix: -0.35 (0.36), residues: 222 sheet: 0.79 (0.27), residues: 339 loop : -0.33 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.015 0.001 TYR C 98 PHE 0.007 0.001 PHE B 56 TRP 0.011 0.001 TRP A 268 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7992) covalent geometry : angle 0.60927 (10878) SS BOND : bond 0.00315 ( 15) SS BOND : angle 0.98554 ( 30) hydrogen bonds : bond 0.03493 ( 196) hydrogen bonds : angle 4.84869 ( 516) link_NAG-ASN : bond 0.00673 ( 9) link_NAG-ASN : angle 2.54295 ( 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 241 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8438 (mtpt) REVERT: A 96 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6686 (tm-30) REVERT: A 220 ASP cc_start: 0.8231 (p0) cc_final: 0.7949 (p0) REVERT: A 273 ASP cc_start: 0.8587 (m-30) cc_final: 0.8338 (m-30) REVERT: B 56 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6955 (t80) REVERT: B 191 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7720 (mtm) REVERT: B 211 SER cc_start: 0.8533 (p) cc_final: 0.8278 (m) REVERT: B 224 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8303 (mtpp) REVERT: B 289 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7262 (t0) REVERT: B 343 ILE cc_start: 0.8373 (mp) cc_final: 0.7968 (tt) REVERT: C 96 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6745 (tm-30) REVERT: C 191 MET cc_start: 0.7900 (mpp) cc_final: 0.7390 (mpp) REVERT: C 211 SER cc_start: 0.8645 (p) cc_final: 0.8385 (m) outliers start: 29 outliers final: 16 residues processed: 225 average time/residue: 0.5015 time to fit residues: 119.4790 Evaluate side-chains 231 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 204 HIS A 280 ASN A 344 ASN B 122 GLN B 204 HIS B 344 ASN C 152 ASN C 204 HIS C 344 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116646 restraints weight = 11092.601| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.06 r_work: 0.3442 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8016 Z= 0.187 Angle : 0.655 9.785 10935 Z= 0.316 Chirality : 0.050 0.342 1239 Planarity : 0.004 0.034 1344 Dihedral : 11.771 82.398 1348 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.25 % Allowed : 19.01 % 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: -0.05 (0.27), residues: 963 helix: -0.48 (0.35), residues: 222 sheet: 0.80 (0.27), residues: 339 loop : -0.37 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.015 0.001 TYR C 222 PHE 0.008 0.001 PHE A 239 TRP 0.010 0.001 TRP B 268 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 7992) covalent geometry : angle 0.63776 (10878) SS BOND : bond 0.00365 ( 15) SS BOND : angle 1.20639 ( 30) hydrogen bonds : bond 0.03897 ( 196) hydrogen bonds : angle 4.95197 ( 516) link_NAG-ASN : bond 0.00614 ( 9) link_NAG-ASN : angle 2.85583 ( 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 240 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8448 (mtpt) REVERT: A 81 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8415 (tttp) REVERT: A 96 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6685 (tm-30) REVERT: A 220 ASP cc_start: 0.8240 (p0) cc_final: 0.7938 (p0) REVERT: A 273 ASP cc_start: 0.8595 (m-30) cc_final: 0.8354 (m-30) REVERT: B 191 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: B 211 SER cc_start: 0.8548 (p) cc_final: 0.8294 (m) REVERT: B 224 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8318 (mtpp) REVERT: B 343 ILE cc_start: 0.8413 (mp) cc_final: 0.7999 (tt) REVERT: C 96 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6719 (tm-30) REVERT: C 191 MET cc_start: 0.7919 (mpp) cc_final: 0.7451 (mpp) REVERT: C 211 SER cc_start: 0.8662 (p) cc_final: 0.8403 (m) outliers start: 27 outliers final: 16 residues processed: 227 average time/residue: 0.5090 time to fit residues: 122.4694 Evaluate side-chains 232 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 87 optimal weight: 0.0070 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 A 280 ASN A 344 ASN B 122 GLN B 204 HIS C 152 ASN C 204 HIS C 344 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117381 restraints weight = 11077.744| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.05 r_work: 0.3455 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1996 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= 0.141 Angle : 0.638 9.673 10935 Z= 0.306 Chirality : 0.049 0.325 1239 Planarity : 0.004 0.035 1344 Dihedral : 10.939 81.519 1346 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.01 % Allowed : 19.98 % Favored : 77.02 % 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 (0.27), residues: 963 helix: -0.55 (0.35), residues: 222 sheet: 0.81 (0.27), residues: 339 loop : -0.34 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.016 0.001 TYR C 98 PHE 0.011 0.001 PHE B 56 TRP 0.012 0.001 TRP A 268 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7992) covalent geometry : angle 0.61797 (10878) SS BOND : bond 0.00303 ( 15) SS BOND : angle 0.99394 ( 30) hydrogen bonds : bond 0.03598 ( 196) hydrogen bonds : angle 4.92909 ( 516) link_NAG-ASN : bond 0.00629 ( 9) link_NAG-ASN : angle 3.16251 ( 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 234 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8443 (mtpt) REVERT: A 96 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6670 (tm-30) REVERT: A 220 ASP cc_start: 0.8212 (p0) cc_final: 0.7933 (p0) REVERT: A 273 ASP cc_start: 0.8583 (m-30) cc_final: 0.8335 (m-30) REVERT: B 191 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: B 211 SER cc_start: 0.8545 (p) cc_final: 0.8289 (m) REVERT: B 224 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8302 (mtpp) REVERT: B 343 ILE cc_start: 0.8368 (mp) cc_final: 0.7922 (tt) REVERT: C 96 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6745 (tm-30) REVERT: C 191 MET cc_start: 0.7886 (mpp) cc_final: 0.7360 (mpp) REVERT: C 211 SER cc_start: 0.8651 (p) cc_final: 0.8395 (m) outliers start: 25 outliers final: 18 residues processed: 220 average time/residue: 0.5110 time to fit residues: 119.1719 Evaluate side-chains 229 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 A 204 HIS A 280 ASN A 344 ASN B 122 GLN B 204 HIS C 152 ASN C 204 HIS C 344 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117041 restraints weight = 10972.145| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.07 r_work: 0.3451 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8016 Z= 0.163 Angle : 0.648 8.825 10935 Z= 0.313 Chirality : 0.049 0.319 1239 Planarity : 0.004 0.035 1344 Dihedral : 10.598 80.953 1346 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.01 % Allowed : 20.10 % Favored : 76.90 % 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: -0.06 (0.27), residues: 963 helix: -0.55 (0.35), residues: 222 sheet: 0.80 (0.27), residues: 339 loop : -0.34 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.015 0.001 TYR C 98 PHE 0.011 0.001 PHE B 56 TRP 0.010 0.001 TRP B 268 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7992) covalent geometry : angle 0.62507 (10878) SS BOND : bond 0.00373 ( 15) SS BOND : angle 1.13607 ( 30) hydrogen bonds : bond 0.03724 ( 196) hydrogen bonds : angle 4.94993 ( 516) link_NAG-ASN : bond 0.00587 ( 9) link_NAG-ASN : angle 3.36952 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3414.09 seconds wall clock time: 58 minutes 38.85 seconds (3518.85 seconds total)