Starting phenix.real_space_refine on Sun Apr 5 04:03:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oir_70527/04_2026/9oir_70527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oir_70527/04_2026/9oir_70527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oir_70527/04_2026/9oir_70527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oir_70527/04_2026/9oir_70527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oir_70527/04_2026/9oir_70527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oir_70527/04_2026/9oir_70527.map" } resolution = 3.0 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= 0.019 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 5031 2.51 5 N 1299 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 7869 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2550 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 310} 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: C, B Time building chain proxies: 1.77, per 1000 atoms: 0.22 Number of scatterers: 7869 At special positions: 0 Unit cell: (88.776, 91.242, 125.766, 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 1491 8.00 N 1299 7.00 C 5031 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=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.04 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 C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 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 194 " " NAG A 504 " - " ASN A 310 " " NAG B 502 " - " ASN B 133 " " NAG B 503 " - " ASN B 194 " " NAG B 504 " - " ASN B 310 " " NAG C 502 " - " ASN C 133 " " NAG C 503 " - " ASN C 194 " " NAG C 504 " - " ASN C 310 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 321.9 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 26.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 40 through 58 removed outlier: 3.876A pdb=" N VAL A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.578A 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 189 through 194 Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.518A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 365 removed outlier: 3.670A pdb=" N THR A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 3.876A pdb=" N VAL C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 56 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.578A 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 189 through 194 Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.519A pdb=" N LEU C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 365 removed outlier: 3.670A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 3.876A pdb=" N VAL B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.578A 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 189 through 194 Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.518A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 365 removed outlier: 3.672A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 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 334 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 'C' and resid 71 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 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 334 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 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 334 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 88 184 hydrogen bonds defined for protein. 480 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: 1.19 Time building geometry restraints manager: 1.04 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: 2448 1.34 - 1.46: 2025 1.46 - 1.58: 3540 1.58 - 1.70: 12 1.70 - 1.82: 45 Bond restraints: 8070 Sorted by residual: bond pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.34e+00 bond pdb=" N VAL B 354 " pdb=" CA VAL B 354 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.08e+00 bond pdb=" N VAL C 354 " pdb=" CA VAL C 354 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.00e+00 bond pdb=" N HIS B 132 " pdb=" CA HIS B 132 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.19e+00 bond pdb=" N HIS C 132 " pdb=" CA HIS C 132 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.98e+00 ... (remaining 8065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10540 1.68 - 3.36: 347 3.36 - 5.05: 72 5.05 - 6.73: 15 6.73 - 8.41: 9 Bond angle restraints: 10983 Sorted by residual: angle pdb=" C ASN C 194 " pdb=" CA ASN C 194 " pdb=" CB ASN C 194 " ideal model delta sigma weight residual 110.56 118.97 -8.41 1.69e+00 3.50e-01 2.48e+01 angle pdb=" C ASN A 194 " pdb=" CA ASN A 194 " pdb=" CB ASN A 194 " ideal model delta sigma weight residual 110.56 118.97 -8.41 1.69e+00 3.50e-01 2.47e+01 angle pdb=" C ASN B 194 " pdb=" CA ASN B 194 " pdb=" CB ASN B 194 " ideal model delta sigma weight residual 110.56 118.95 -8.39 1.69e+00 3.50e-01 2.47e+01 angle pdb=" CA PHE A 61 " pdb=" CB PHE A 61 " pdb=" CG PHE A 61 " ideal model delta sigma weight residual 113.80 118.67 -4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" CA PHE C 61 " pdb=" CB PHE C 61 " pdb=" CG PHE C 61 " ideal model delta sigma weight residual 113.80 118.67 -4.87 1.00e+00 1.00e+00 2.37e+01 ... (remaining 10978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4237 16.94 - 33.88: 451 33.88 - 50.81: 187 50.81 - 67.75: 45 67.75 - 84.69: 9 Dihedral angle restraints: 4929 sinusoidal: 2121 harmonic: 2808 Sorted by residual: dihedral pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -162.53 76.53 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " pdb=" SG CYS C 159 " pdb=" CB CYS C 159 " ideal model delta sinusoidal sigma weight residual -86.00 -162.53 76.53 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -162.53 76.53 1 1.00e+01 1.00e-02 7.36e+01 ... (remaining 4926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 961 0.054 - 0.108: 217 0.108 - 0.162: 55 0.162 - 0.215: 17 0.215 - 0.269: 4 Chirality restraints: 1254 Sorted by residual: chirality pdb=" C1 NAG C 504 " pdb=" ND2 ASN C 310 " pdb=" C2 NAG C 504 " pdb=" O5 NAG C 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 310 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 310 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1251 not shown) Planarity restraints: 1365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 502 " -0.245 2.00e-02 2.50e+03 2.08e-01 5.39e+02 pdb=" C7 NAG A 502 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A 502 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG A 502 " 0.356 2.00e-02 2.50e+03 pdb=" O7 NAG A 502 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " -0.245 2.00e-02 2.50e+03 2.08e-01 5.39e+02 pdb=" C7 NAG B 502 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " 0.356 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.244 2.00e-02 2.50e+03 2.07e-01 5.38e+02 pdb=" C7 NAG C 502 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " -0.011 2.00e-02 2.50e+03 ... (remaining 1362 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1632 2.78 - 3.31: 6838 3.31 - 3.84: 12332 3.84 - 4.37: 13976 4.37 - 4.90: 25331 Nonbonded interactions: 60109 Sorted by model distance: nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.255 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.256 3.040 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.256 3.040 nonbonded pdb=" O SER B 119 " pdb=" OG SER B 119 " model vdw 2.301 3.040 nonbonded pdb=" O SER C 119 " pdb=" OG SER C 119 " model vdw 2.301 3.040 ... (remaining 60104 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 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.030 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: 0.030 Set scattering table: 0.020 Process input model: 9.050 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 0.037 8094 Z= 0.235 Angle : 0.748 8.409 11040 Z= 0.422 Chirality : 0.054 0.269 1254 Planarity : 0.011 0.208 1356 Dihedral : 16.815 84.689 3096 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.48 % Allowed : 27.02 % Favored : 72.50 % 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: -0.37 (0.25), residues: 972 helix: -0.53 (0.34), residues: 195 sheet: 1.42 (0.29), residues: 300 loop : -1.26 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 287 TYR 0.015 0.001 TYR B 98 PHE 0.018 0.002 PHE C 228 TRP 0.008 0.001 TRP C 268 HIS 0.002 0.000 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8070) covalent geometry : angle 0.73875 (10983) SS BOND : bond 0.00376 ( 15) SS BOND : angle 1.42862 ( 30) hydrogen bonds : bond 0.19868 ( 184) hydrogen bonds : angle 8.23650 ( 480) link_NAG-ASN : bond 0.00959 ( 9) link_NAG-ASN : angle 2.16447 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 306 TYR cc_start: 0.8451 (m-80) cc_final: 0.8159 (m-80) REVERT: C 156 THR cc_start: 0.8306 (t) cc_final: 0.8080 (p) REVERT: C 258 LYS cc_start: 0.7966 (mmmm) cc_final: 0.7579 (mmmm) REVERT: B 97 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 191 MET cc_start: 0.7411 (mtm) cc_final: 0.6983 (mtm) REVERT: B 305 LYS cc_start: 0.8249 (mttp) cc_final: 0.7901 (mtpp) REVERT: B 349 LEU cc_start: 0.7624 (mt) cc_final: 0.7407 (mm) outliers start: 4 outliers final: 0 residues processed: 180 average time/residue: 0.4827 time to fit residues: 92.8756 Evaluate side-chains 161 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN B 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117360 restraints weight = 11037.346| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.19 r_work: 0.3410 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8094 Z= 0.212 Angle : 0.658 7.238 11040 Z= 0.342 Chirality : 0.050 0.148 1254 Planarity : 0.005 0.045 1356 Dihedral : 9.985 89.802 1350 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.60 % Allowed : 22.98 % Favored : 71.43 % 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: -0.17 (0.26), residues: 972 helix: 0.10 (0.36), residues: 195 sheet: 1.27 (0.29), residues: 300 loop : -1.15 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.016 0.002 TYR A 321 PHE 0.021 0.002 PHE A 336 TRP 0.016 0.001 TRP C 268 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 8070) covalent geometry : angle 0.65002 (10983) SS BOND : bond 0.00503 ( 15) SS BOND : angle 1.70398 ( 30) hydrogen bonds : bond 0.05001 ( 184) hydrogen bonds : angle 6.48917 ( 480) link_NAG-ASN : bond 0.00197 ( 9) link_NAG-ASN : angle 1.44581 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8729 (t) cc_final: 0.8495 (p) REVERT: A 278 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7901 (mm-30) REVERT: A 306 TYR cc_start: 0.8621 (m-80) cc_final: 0.8402 (m-80) REVERT: C 137 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7642 (mm) REVERT: C 179 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: C 258 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7917 (mmmm) REVERT: B 97 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 179 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: B 255 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7563 (mt) REVERT: B 278 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 305 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (mtmm) outliers start: 47 outliers final: 16 residues processed: 189 average time/residue: 0.4237 time to fit residues: 86.4092 Evaluate side-chains 181 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 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 152 ASN C 64 GLN C 152 ASN B 122 GLN B 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117807 restraints weight = 11046.573| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.17 r_work: 0.3420 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8094 Z= 0.173 Angle : 0.621 7.454 11040 Z= 0.322 Chirality : 0.048 0.144 1254 Planarity : 0.004 0.040 1356 Dihedral : 9.979 89.206 1350 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.52 % Allowed : 25.48 % Favored : 70.00 % 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 (0.26), residues: 972 helix: 0.30 (0.37), residues: 195 sheet: 1.22 (0.29), residues: 300 loop : -1.04 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.014 0.001 TYR A 321 PHE 0.018 0.002 PHE A 336 TRP 0.014 0.001 TRP C 268 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8070) covalent geometry : angle 0.61498 (10983) SS BOND : bond 0.00414 ( 15) SS BOND : angle 1.56635 ( 30) hydrogen bonds : bond 0.04267 ( 184) hydrogen bonds : angle 6.01657 ( 480) link_NAG-ASN : bond 0.00088 ( 9) link_NAG-ASN : angle 1.16395 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8657 (t) cc_final: 0.8394 (p) REVERT: A 184 VAL cc_start: 0.8329 (t) cc_final: 0.8062 (m) REVERT: A 306 TYR cc_start: 0.8618 (m-80) cc_final: 0.8381 (m-80) REVERT: C 119 SER cc_start: 0.8570 (t) cc_final: 0.8306 (p) REVERT: C 255 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7865 (mt) REVERT: B 97 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 156 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 179 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: B 255 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7529 (mt) REVERT: B 305 LYS cc_start: 0.8400 (mttp) cc_final: 0.8153 (mtmm) REVERT: B 358 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8161 (mm) outliers start: 38 outliers final: 16 residues processed: 185 average time/residue: 0.4427 time to fit residues: 87.9337 Evaluate side-chains 188 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 49 optimal weight: 0.0040 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 28 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.1970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 257 HIS C 152 ASN B 122 GLN B 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120021 restraints weight = 11171.451| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.26 r_work: 0.3451 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8094 Z= 0.095 Angle : 0.560 7.535 11040 Z= 0.286 Chirality : 0.045 0.135 1254 Planarity : 0.004 0.036 1356 Dihedral : 9.433 84.657 1350 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.57 % Allowed : 26.43 % Favored : 70.00 % 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: 0.12 (0.26), residues: 972 helix: 0.57 (0.38), residues: 195 sheet: 1.28 (0.30), residues: 300 loop : -0.95 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 158 TYR 0.013 0.001 TYR A 45 PHE 0.011 0.001 PHE C 228 TRP 0.007 0.001 TRP C 93 HIS 0.001 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8070) covalent geometry : angle 0.55574 (10983) SS BOND : bond 0.00312 ( 15) SS BOND : angle 1.22926 ( 30) hydrogen bonds : bond 0.03368 ( 184) hydrogen bonds : angle 5.45227 ( 480) link_NAG-ASN : bond 0.00170 ( 9) link_NAG-ASN : angle 0.82952 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8567 (t) cc_final: 0.8235 (p) REVERT: A 184 VAL cc_start: 0.8251 (t) cc_final: 0.7977 (m) REVERT: A 306 TYR cc_start: 0.8642 (m-80) cc_final: 0.8401 (m-80) REVERT: C 119 SER cc_start: 0.8453 (t) cc_final: 0.8153 (p) REVERT: C 228 PHE cc_start: 0.8186 (t80) cc_final: 0.7949 (t80) REVERT: C 254 GLU cc_start: 0.7647 (mp0) cc_final: 0.7160 (mp0) REVERT: B 97 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7503 (mt-10) REVERT: B 156 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8369 (t) REVERT: B 305 LYS cc_start: 0.8376 (mttp) cc_final: 0.8117 (mtpp) REVERT: B 316 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8178 (p) outliers start: 30 outliers final: 15 residues processed: 185 average time/residue: 0.4384 time to fit residues: 87.3055 Evaluate side-chains 189 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 122 GLN B 204 HIS 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 = 0.133862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119023 restraints weight = 11186.873| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.15 r_work: 0.3441 rms_B_bonded: 2.43 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: 0.7716 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8094 Z= 0.137 Angle : 0.581 7.507 11040 Z= 0.298 Chirality : 0.047 0.136 1254 Planarity : 0.004 0.034 1356 Dihedral : 9.509 82.836 1350 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.64 % Allowed : 26.55 % Favored : 68.81 % 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 (0.26), residues: 972 helix: 0.61 (0.38), residues: 195 sheet: 1.29 (0.30), residues: 300 loop : -0.91 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.015 0.001 TYR C 321 PHE 0.013 0.002 PHE A 336 TRP 0.011 0.001 TRP C 268 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8070) covalent geometry : angle 0.57592 (10983) SS BOND : bond 0.00360 ( 15) SS BOND : angle 1.33073 ( 30) hydrogen bonds : bond 0.03639 ( 184) hydrogen bonds : angle 5.55492 ( 480) link_NAG-ASN : bond 0.00075 ( 9) link_NAG-ASN : angle 1.02191 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8584 (t) cc_final: 0.8250 (p) REVERT: A 184 VAL cc_start: 0.8282 (t) cc_final: 0.8036 (m) REVERT: A 306 TYR cc_start: 0.8624 (m-80) cc_final: 0.8378 (m-80) REVERT: C 119 SER cc_start: 0.8495 (t) cc_final: 0.8158 (p) REVERT: C 127 GLU cc_start: 0.7637 (tp30) cc_final: 0.7096 (tp30) REVERT: C 152 ASN cc_start: 0.8564 (m110) cc_final: 0.8146 (p0) REVERT: C 228 PHE cc_start: 0.8192 (t80) cc_final: 0.7979 (t80) REVERT: C 254 GLU cc_start: 0.7697 (mp0) cc_final: 0.7138 (mp0) REVERT: B 97 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7510 (mt-10) REVERT: B 156 THR cc_start: 0.8627 (p) cc_final: 0.8423 (t) REVERT: B 179 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: B 250 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6397 (mm-30) REVERT: B 305 LYS cc_start: 0.8386 (mttp) cc_final: 0.8156 (mtpp) REVERT: B 316 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8204 (p) outliers start: 39 outliers final: 19 residues processed: 196 average time/residue: 0.4243 time to fit residues: 89.5839 Evaluate side-chains 195 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 122 GLN B 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119713 restraints weight = 11212.797| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.16 r_work: 0.3453 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8094 Z= 0.111 Angle : 0.565 7.582 11040 Z= 0.287 Chirality : 0.046 0.130 1254 Planarity : 0.004 0.034 1356 Dihedral : 9.318 80.265 1350 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.40 % Allowed : 26.31 % Favored : 69.29 % 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: 0.28 (0.26), residues: 972 helix: 0.77 (0.39), residues: 195 sheet: 1.37 (0.30), residues: 300 loop : -0.85 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 155 TYR 0.015 0.001 TYR C 321 PHE 0.009 0.001 PHE A 336 TRP 0.008 0.001 TRP C 268 HIS 0.001 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8070) covalent geometry : angle 0.56115 (10983) SS BOND : bond 0.00324 ( 15) SS BOND : angle 1.21630 ( 30) hydrogen bonds : bond 0.03333 ( 184) hydrogen bonds : angle 5.36188 ( 480) link_NAG-ASN : bond 0.00108 ( 9) link_NAG-ASN : angle 0.93350 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8545 (t) cc_final: 0.8189 (p) REVERT: A 184 VAL cc_start: 0.8243 (t) cc_final: 0.7991 (m) REVERT: A 306 TYR cc_start: 0.8623 (m-80) cc_final: 0.8349 (m-80) REVERT: C 228 PHE cc_start: 0.8175 (t80) cc_final: 0.7972 (t80) REVERT: C 254 GLU cc_start: 0.7705 (mp0) cc_final: 0.7133 (mp0) REVERT: C 278 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 97 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 179 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: B 250 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6337 (mm-30) REVERT: B 305 LYS cc_start: 0.8363 (mttp) cc_final: 0.8116 (mtpp) REVERT: B 316 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8172 (p) outliers start: 37 outliers final: 17 residues processed: 192 average time/residue: 0.4386 time to fit residues: 90.6708 Evaluate side-chains 189 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN B 122 GLN B 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119009 restraints weight = 11109.207| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.14 r_work: 0.3441 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8094 Z= 0.144 Angle : 0.587 7.818 11040 Z= 0.299 Chirality : 0.047 0.130 1254 Planarity : 0.004 0.035 1356 Dihedral : 9.423 80.560 1350 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.05 % Allowed : 26.79 % Favored : 69.17 % 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: 972 helix: 0.79 (0.39), residues: 195 sheet: 1.36 (0.30), residues: 300 loop : -0.91 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.015 0.001 TYR C 321 PHE 0.014 0.002 PHE A 336 TRP 0.012 0.001 TRP C 268 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8070) covalent geometry : angle 0.58214 (10983) SS BOND : bond 0.00362 ( 15) SS BOND : angle 1.33959 ( 30) hydrogen bonds : bond 0.03544 ( 184) hydrogen bonds : angle 5.47892 ( 480) link_NAG-ASN : bond 0.00074 ( 9) link_NAG-ASN : angle 1.06322 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8594 (t) cc_final: 0.8253 (p) REVERT: A 184 VAL cc_start: 0.8246 (t) cc_final: 0.7996 (m) REVERT: A 306 TYR cc_start: 0.8611 (m-80) cc_final: 0.8326 (m-80) REVERT: C 119 SER cc_start: 0.8459 (t) cc_final: 0.8212 (p) REVERT: C 152 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8118 (p0) REVERT: C 228 PHE cc_start: 0.8147 (t80) cc_final: 0.7905 (t80) REVERT: C 254 GLU cc_start: 0.7698 (mp0) cc_final: 0.7074 (mp0) REVERT: C 278 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: C 321 TYR cc_start: 0.8191 (m-80) cc_final: 0.7667 (m-80) REVERT: B 97 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 179 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: B 250 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6386 (mm-30) REVERT: B 305 LYS cc_start: 0.8350 (mttp) cc_final: 0.8040 (mtmp) outliers start: 34 outliers final: 22 residues processed: 185 average time/residue: 0.4481 time to fit residues: 89.0233 Evaluate side-chains 190 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 0.0670 chunk 46 optimal weight: 0.0770 chunk 74 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 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 152 ASN B 122 GLN B 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118865 restraints weight = 11199.859| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.27 r_work: 0.3437 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8094 Z= 0.129 Angle : 0.589 8.145 11040 Z= 0.299 Chirality : 0.047 0.132 1254 Planarity : 0.004 0.034 1356 Dihedral : 9.356 79.610 1350 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.40 % Allowed : 27.26 % Favored : 68.33 % 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: 972 helix: 0.82 (0.39), residues: 195 sheet: 1.36 (0.30), residues: 300 loop : -0.92 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.014 0.001 TYR C 321 PHE 0.012 0.001 PHE A 336 TRP 0.010 0.001 TRP C 268 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8070) covalent geometry : angle 0.58462 (10983) SS BOND : bond 0.00334 ( 15) SS BOND : angle 1.28868 ( 30) hydrogen bonds : bond 0.03408 ( 184) hydrogen bonds : angle 5.39667 ( 480) link_NAG-ASN : bond 0.00088 ( 9) link_NAG-ASN : angle 1.00110 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8605 (t) cc_final: 0.8256 (p) REVERT: A 184 VAL cc_start: 0.8289 (t) cc_final: 0.8033 (m) REVERT: A 306 TYR cc_start: 0.8634 (m-80) cc_final: 0.8372 (m-80) REVERT: C 119 SER cc_start: 0.8483 (t) cc_final: 0.8239 (p) REVERT: C 228 PHE cc_start: 0.8172 (t80) cc_final: 0.7969 (t80) REVERT: C 254 GLU cc_start: 0.7744 (mp0) cc_final: 0.7159 (mp0) REVERT: B 97 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 179 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: B 250 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6423 (mm-30) REVERT: B 305 LYS cc_start: 0.8383 (mttp) cc_final: 0.8103 (mtpp) outliers start: 37 outliers final: 23 residues processed: 188 average time/residue: 0.4561 time to fit residues: 92.0395 Evaluate side-chains 192 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 87 optimal weight: 0.2980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 152 ASN B 122 GLN B 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120018 restraints weight = 11143.163| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.24 r_work: 0.3449 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8094 Z= 0.108 Angle : 0.575 8.413 11040 Z= 0.291 Chirality : 0.046 0.127 1254 Planarity : 0.004 0.031 1356 Dihedral : 9.139 78.035 1350 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.05 % Allowed : 27.74 % Favored : 68.21 % 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: 0.35 (0.26), residues: 972 helix: 0.95 (0.39), residues: 195 sheet: 1.42 (0.30), residues: 300 loop : -0.88 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 324 TYR 0.018 0.001 TYR C 321 PHE 0.008 0.001 PHE A 336 TRP 0.008 0.001 TRP C 268 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8070) covalent geometry : angle 0.57097 (10983) SS BOND : bond 0.00314 ( 15) SS BOND : angle 1.20660 ( 30) hydrogen bonds : bond 0.03148 ( 184) hydrogen bonds : angle 5.22137 ( 480) link_NAG-ASN : bond 0.00123 ( 9) link_NAG-ASN : angle 0.93670 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8558 (t) cc_final: 0.8207 (p) REVERT: A 184 VAL cc_start: 0.8271 (t) cc_final: 0.8023 (m) REVERT: C 119 SER cc_start: 0.8427 (t) cc_final: 0.8151 (p) REVERT: C 228 PHE cc_start: 0.8177 (t80) cc_final: 0.7936 (t80) REVERT: C 254 GLU cc_start: 0.7712 (mp0) cc_final: 0.7148 (mp0) REVERT: B 97 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7570 (mt-10) REVERT: B 143 VAL cc_start: 0.8143 (p) cc_final: 0.7914 (m) REVERT: B 179 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: B 250 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6341 (mm-30) REVERT: B 305 LYS cc_start: 0.8381 (mttp) cc_final: 0.8103 (mtpp) outliers start: 34 outliers final: 24 residues processed: 189 average time/residue: 0.4497 time to fit residues: 91.2568 Evaluate side-chains 183 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119868 restraints weight = 11097.035| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.27 r_work: 0.3443 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 8094 Z= 0.198 Angle : 1.177 59.200 11040 Z= 0.714 Chirality : 0.047 0.247 1254 Planarity : 0.004 0.031 1356 Dihedral : 9.140 78.036 1350 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.98 % Allowed : 28.93 % Favored : 68.10 % Cbeta Deviations : 0.22 % 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: 0.36 (0.26), residues: 972 helix: 0.93 (0.39), residues: 195 sheet: 1.43 (0.30), residues: 300 loop : -0.87 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 287 TYR 0.018 0.001 TYR C 321 PHE 0.010 0.001 PHE A 336 TRP 0.008 0.001 TRP C 268 HIS 0.002 0.000 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8070) covalent geometry : angle 1.17803 (10983) SS BOND : bond 0.00387 ( 15) SS BOND : angle 1.19556 ( 30) hydrogen bonds : bond 0.03197 ( 184) hydrogen bonds : angle 5.22122 ( 480) link_NAG-ASN : bond 0.00166 ( 9) link_NAG-ASN : angle 0.90378 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 SER cc_start: 0.8561 (t) cc_final: 0.8217 (p) REVERT: A 184 VAL cc_start: 0.8286 (t) cc_final: 0.8039 (m) REVERT: A 321 TYR cc_start: 0.8313 (m-80) cc_final: 0.8080 (m-80) REVERT: C 119 SER cc_start: 0.8445 (t) cc_final: 0.8170 (p) REVERT: C 228 PHE cc_start: 0.8208 (t80) cc_final: 0.7964 (t80) REVERT: C 254 GLU cc_start: 0.7756 (mp0) cc_final: 0.7189 (mp0) REVERT: B 97 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 143 VAL cc_start: 0.8171 (p) cc_final: 0.7936 (m) REVERT: B 179 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: B 250 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6363 (mm-30) REVERT: B 305 LYS cc_start: 0.8393 (mttp) cc_final: 0.8130 (mtpp) outliers start: 25 outliers final: 21 residues processed: 173 average time/residue: 0.4324 time to fit residues: 80.4142 Evaluate side-chains 179 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 122 GLN B 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.119497 restraints weight = 11145.355| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.26 r_work: 0.3432 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 8094 Z= 0.198 Angle : 1.177 59.200 11040 Z= 0.714 Chirality : 0.047 0.247 1254 Planarity : 0.004 0.031 1356 Dihedral : 9.140 78.036 1350 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 29.29 % Favored : 68.10 % Cbeta Deviations : 0.22 % 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: 0.36 (0.26), residues: 972 helix: 0.93 (0.39), residues: 195 sheet: 1.43 (0.30), residues: 300 loop : -0.87 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 287 TYR 0.018 0.001 TYR C 321 PHE 0.010 0.001 PHE A 336 TRP 0.008 0.001 TRP C 268 HIS 0.002 0.000 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8070) covalent geometry : angle 1.17803 (10983) SS BOND : bond 0.00387 ( 15) SS BOND : angle 1.19556 ( 30) hydrogen bonds : bond 0.03197 ( 184) hydrogen bonds : angle 5.22122 ( 480) link_NAG-ASN : bond 0.00166 ( 9) link_NAG-ASN : angle 0.90378 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2928.40 seconds wall clock time: 50 minutes 36.32 seconds (3036.32 seconds total)