Starting phenix.real_space_refine on Thu Oct 22 20:15:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x35_66494/10_2026/9x35_66494.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x35_66494/10_2026/9x35_66494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x35_66494/10_2026/9x35_66494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x35_66494/10_2026/9x35_66494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x35_66494/10_2026/9x35_66494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x35_66494/10_2026/9x35_66494.map" } resolution = 2.81 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= 0.026 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 3083 2.51 5 N 797 2.21 5 O 967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4863 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1345 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1656 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 192} Chain: "C" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1673 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 0.97, per 1000 atoms: 0.20 Number of scatterers: 4863 At special positions: 0 Unit cell: (67.064, 80.8, 123.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 967 8.00 N 797 7.00 C 3083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 425 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG D 1 " - " ASN A 162 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN B 297 " " NAG G 1 " - " ASN C 297 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 228.6 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 16 sheets defined 13.1% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.755A pdb=" N SER A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.688A pdb=" N LEU B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 355 through 360 removed outlier: 3.595A pdb=" N THR B 359 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.576A pdb=" N LEU C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.649A pdb=" N GLY C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 436 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.593A pdb=" N VAL A 9 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.465A pdb=" N LEU A 157 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS A 120 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS A 119 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS A 134 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 121 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR A 132 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A 123 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 239 through 243 removed outlier: 3.699A pdb=" N ASP B 265 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 300 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 243 removed outlier: 3.699A pdb=" N ASP B 265 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 300 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 282 through 284 removed outlier: 4.391A pdb=" N TRP B 277 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.553A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.553A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 386 through 388 removed outlier: 4.476A pdb=" N TRP B 381 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 239 through 243 removed outlier: 5.569A pdb=" N THR C 260 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU C 306 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL C 262 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER C 304 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL C 264 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C 302 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 282 through 284 removed outlier: 4.380A pdb=" N TRP C 277 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.659A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 347 through 351 removed outlier: 5.659A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 386 through 387 243 hydrogen bonds defined for protein. 570 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: 0.69 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1518 1.34 - 1.46: 1146 1.46 - 1.58: 2304 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4988 Sorted by residual: bond pdb=" C5 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.418 1.457 -0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.450 -0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 MAN F 5 " pdb=" C2 MAN F 5 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " ideal model delta sigma weight residual 1.526 1.553 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.544 -0.025 2.00e-02 2.50e+03 1.53e+00 ... (remaining 4983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6606 1.77 - 3.53: 147 3.53 - 5.30: 29 5.30 - 7.06: 12 7.06 - 8.83: 1 Bond angle restraints: 6795 Sorted by residual: angle pdb=" C LEU B 242 " pdb=" N LEU B 243 " pdb=" CA LEU B 243 " ideal model delta sigma weight residual 121.83 130.66 -8.83 1.56e+00 4.11e-01 3.20e+01 angle pdb=" C LEU C 242 " pdb=" N LEU C 243 " pdb=" CA LEU C 243 " ideal model delta sigma weight residual 121.83 127.73 -5.90 1.56e+00 4.11e-01 1.43e+01 angle pdb=" C THR C 393 " pdb=" N THR C 394 " pdb=" CA THR C 394 " ideal model delta sigma weight residual 120.49 124.94 -4.45 1.42e+00 4.96e-01 9.81e+00 angle pdb=" CA GLY B 341 " pdb=" C GLY B 341 " pdb=" N GLN B 342 " ideal model delta sigma weight residual 115.11 117.29 -2.18 9.50e-01 1.11e+00 5.25e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.41 6.54 3.00e+00 1.11e-01 4.76e+00 ... (remaining 6790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 3033 23.92 - 47.85: 118 47.85 - 71.77: 15 71.77 - 95.69: 20 95.69 - 119.61: 13 Dihedral angle restraints: 3199 sinusoidal: 1469 harmonic: 1730 Sorted by residual: dihedral pdb=" C2 MAN G 5 " pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " pdb=" C5 MAN G 5 " ideal model delta sinusoidal sigma weight residual -57.62 61.99 -119.61 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.89 109.82 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.72 108.43 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 3196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 647 0.055 - 0.110: 127 0.110 - 0.165: 23 0.165 - 0.220: 1 0.220 - 0.275: 3 Chirality restraints: 801 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 798 not shown) Planarity restraints: 850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 342 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO C 343 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 98 " -0.012 2.00e-02 2.50e+03 1.02e-02 2.58e+00 pdb=" CG TRP A 98 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 98 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 98 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 98 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 98 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 98 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 98 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 98 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 237 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 238 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " 0.016 5.00e-02 4.00e+02 ... (remaining 847 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1166 2.80 - 3.33: 3900 3.33 - 3.85: 7996 3.85 - 4.38: 9726 4.38 - 4.90: 16600 Nonbonded interactions: 39388 Sorted by model distance: nonbonded pdb=" OE2 GLU C 382 " pdb=" NE2 GLN C 438 " model vdw 2.281 3.120 nonbonded pdb=" O6 NAG D 2 " pdb=" O6 NAG F 1 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR B 436 " pdb=" OE1 GLN B 438 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP B 401 " pdb=" OG SER B 403 " model vdw 2.337 3.040 nonbonded pdb=" OE2 GLU C 382 " pdb=" OG SER C 426 " model vdw 2.362 3.040 ... (remaining 39383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 235 through 444) } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 1.340 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 0.039 5009 Z= 0.191 Angle : 0.703 8.830 6852 Z= 0.337 Chirality : 0.048 0.275 801 Planarity : 0.004 0.068 846 Dihedral : 16.499 119.615 2059 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.33), residues: 580 helix: -0.21 (0.89), residues: 37 sheet: 1.47 (0.29), residues: 254 loop : 1.15 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.010 0.001 TYR B 407 PHE 0.011 0.002 PHE B 241 TRP 0.027 0.001 TRP A 98 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 4988) covalent geometry : angle 0.68877 / 0.33 ( 6795) SS BOND : bond 0.00202 / 0.13 ( 6) SS BOND : angle 0.50772 / 0.30 ( 12) hydrogen bonds : bond 0.13966 / 8.77 ( 195) hydrogen bonds : angle 5.35892 / 3.76 ( 570) link_ALPHA1-3 : bond 0.00292 / 0.20 ( 2) link_ALPHA1-3 : angle 2.05015 / 1.37 ( 6) link_ALPHA1-6 : bond 0.00276 / 0.19 ( 2) link_ALPHA1-6 : angle 1.61186 / 1.05 ( 6) link_BETA1-4 : bond 0.00328 / 0.21 ( 7) link_BETA1-4 : angle 1.82514 / 1.14 ( 21) link_NAG-ASN : bond 0.00138 / 0.08 ( 4) link_NAG-ASN : angle 1.94305 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.152 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4685 time to fit residues: 62.1884 Evaluate side-chains 111 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [54, 24, 48, 56, 26, 2, 16, 32, 31, 25, 50] chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.0060 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS B 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102518 restraints weight = 7113.730| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.11 r_work: 0.3247 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5009 Z= 0.155 Angle : 0.604 9.573 6852 Z= 0.288 Chirality : 0.044 0.134 801 Planarity : 0.004 0.052 846 Dihedral : 13.449 105.215 926 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.69 % Allowed : 9.57 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.34), residues: 580 helix: -0.34 (0.82), residues: 43 sheet: 1.57 (0.29), residues: 253 loop : 1.09 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.011 0.001 TYR B 407 PHE 0.019 0.002 PHE A 57 TRP 0.011 0.001 TRP A 98 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 4988) covalent geometry : angle 0.57902 / 0.28 ( 6795) SS BOND : bond 0.00238 / 0.14 ( 6) SS BOND : angle 0.49275 / 0.26 ( 12) hydrogen bonds : bond 0.03652 / 2.36 ( 195) hydrogen bonds : angle 4.54692 / 3.12 ( 570) link_ALPHA1-3 : bond 0.00596 / 0.40 ( 2) link_ALPHA1-3 : angle 2.49410 / 1.61 ( 6) link_ALPHA1-6 : bond 0.00561 / 0.39 ( 2) link_ALPHA1-6 : angle 2.84163 / 1.67 ( 6) link_BETA1-4 : bond 0.00294 / 0.19 ( 7) link_BETA1-4 : angle 2.09279 / 1.26 ( 21) link_NAG-ASN : bond 0.00133 / 0.07 ( 4) link_NAG-ASN : angle 1.79167 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.238 Fit side-chains REVERT: B 326 LYS cc_start: 0.8194 (tppp) cc_final: 0.7890 (mttp) REVERT: B 340 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8167 (mttp) REVERT: C 251 LEU cc_start: 0.8551 (mt) cc_final: 0.8299 (mm) REVERT: C 267 SER cc_start: 0.7867 (p) cc_final: 0.7532 (p) REVERT: C 288 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7964 (mtpt) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 0.4752 time to fit residues: 55.6627 Evaluate side-chains 103 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 411 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [42, 31, 7, 30, 15, 27, 11, 53, 3, 33, 2] chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101395 restraints weight = 7037.094| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.10 r_work: 0.3229 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5009 Z= 0.181 Angle : 0.605 8.857 6852 Z= 0.285 Chirality : 0.044 0.201 801 Planarity : 0.004 0.045 846 Dihedral : 9.245 85.770 926 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.88 % Allowed : 12.01 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.34), residues: 580 helix: 0.06 (0.86), residues: 43 sheet: 1.57 (0.30), residues: 253 loop : 1.01 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.014 0.002 TYR B 407 PHE 0.014 0.002 PHE A 158 TRP 0.008 0.001 TRP C 381 HIS 0.005 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 4988) covalent geometry : angle 0.58431 / 0.28 ( 6795) SS BOND : bond 0.00217 / 0.12 ( 6) SS BOND : angle 0.48714 / 0.27 ( 12) hydrogen bonds : bond 0.03675 / 2.38 ( 195) hydrogen bonds : angle 4.49718 / 3.07 ( 570) link_ALPHA1-3 : bond 0.01053 / 0.72 ( 2) link_ALPHA1-3 : angle 1.29643 / 0.85 ( 6) link_ALPHA1-6 : bond 0.01227 / 0.83 ( 2) link_ALPHA1-6 : angle 2.59572 / 1.73 ( 6) link_BETA1-4 : bond 0.00292 / 0.19 ( 7) link_BETA1-4 : angle 2.08652 / 1.22 ( 21) link_NAG-ASN : bond 0.00172 / 0.11 ( 4) link_NAG-ASN : angle 1.97577 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.210 Fit side-chains REVERT: B 340 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8159 (mttp) REVERT: C 267 SER cc_start: 0.7839 (p) cc_final: 0.7578 (p) REVERT: C 288 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7950 (mttm) REVERT: C 318 GLU cc_start: 0.7069 (pp20) cc_final: 0.6508 (pp20) REVERT: C 407 TYR cc_start: 0.8765 (m-80) cc_final: 0.8403 (m-80) outliers start: 10 outliers final: 3 residues processed: 107 average time/residue: 0.4142 time to fit residues: 46.6622 Evaluate side-chains 119 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [54, 30, 15, 4, 37, 22, 52, 48, 0, 19, 42] chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099846 restraints weight = 6835.582| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.17 r_work: 0.3199 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5009 Z= 0.183 Angle : 0.578 8.057 6852 Z= 0.278 Chirality : 0.044 0.144 801 Planarity : 0.004 0.041 846 Dihedral : 6.883 38.998 926 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.25 % Allowed : 12.01 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.34), residues: 580 helix: 0.28 (0.86), residues: 44 sheet: 1.60 (0.30), residues: 257 loop : 0.92 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.014 0.002 TYR B 407 PHE 0.029 0.002 PHE A 57 TRP 0.007 0.001 TRP C 381 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 4988) covalent geometry : angle 0.56157 / 0.27 ( 6795) SS BOND : bond 0.00231 / 0.13 ( 6) SS BOND : angle 0.44531 / 0.25 ( 12) hydrogen bonds : bond 0.03434 / 2.21 ( 195) hydrogen bonds : angle 4.42155 / 3.02 ( 570) link_ALPHA1-3 : bond 0.00975 / 0.67 ( 2) link_ALPHA1-3 : angle 1.59595 / 1.06 ( 6) link_ALPHA1-6 : bond 0.01368 / 0.97 ( 2) link_ALPHA1-6 : angle 1.27416 / 0.71 ( 6) link_BETA1-4 : bond 0.00268 / 0.17 ( 7) link_BETA1-4 : angle 1.89041 / 1.14 ( 21) link_NAG-ASN : bond 0.00158 / 0.10 ( 4) link_NAG-ASN : angle 1.96689 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: B 414 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7954 (ttmt) REVERT: C 267 SER cc_start: 0.7771 (p) cc_final: 0.7515 (p) REVERT: C 288 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8004 (mtpt) REVERT: C 318 GLU cc_start: 0.7124 (pp20) cc_final: 0.6669 (pp20) REVERT: C 365 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8143 (mt) REVERT: C 407 TYR cc_start: 0.8772 (m-80) cc_final: 0.8384 (m-80) outliers start: 12 outliers final: 7 residues processed: 126 average time/residue: 0.4692 time to fit residues: 61.8966 Evaluate side-chains 123 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [8, 26, 25, 52, 9, 43, 42, 19, 12, 38, 53] chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100672 restraints weight = 6996.610| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.19 r_work: 0.3205 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5009 Z= 0.132 Angle : 0.538 8.443 6852 Z= 0.259 Chirality : 0.042 0.126 801 Planarity : 0.004 0.039 846 Dihedral : 5.673 35.806 926 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.06 % Allowed : 13.88 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.34), residues: 580 helix: 0.43 (0.88), residues: 43 sheet: 1.57 (0.30), residues: 257 loop : 0.98 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.011 0.001 TYR B 407 PHE 0.020 0.002 PHE A 57 TRP 0.005 0.001 TRP C 381 HIS 0.003 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4988) covalent geometry : angle 0.52306 / 0.26 ( 6795) SS BOND : bond 0.00108 / 0.06 ( 6) SS BOND : angle 0.33505 / 0.19 ( 12) hydrogen bonds : bond 0.03130 / 2.02 ( 195) hydrogen bonds : angle 4.25153 / 2.92 ( 570) link_ALPHA1-3 : bond 0.01108 / 0.76 ( 2) link_ALPHA1-3 : angle 1.24718 / 0.82 ( 6) link_ALPHA1-6 : bond 0.00839 / 0.58 ( 2) link_ALPHA1-6 : angle 1.38429 / 0.79 ( 6) link_BETA1-4 : bond 0.00307 / 0.19 ( 7) link_BETA1-4 : angle 1.71583 / 1.02 ( 21) link_NAG-ASN : bond 0.00102 / 0.06 ( 4) link_NAG-ASN : angle 1.79749 / 0.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: B 326 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7922 (mttp) REVERT: B 340 LYS cc_start: 0.8466 (ttmm) cc_final: 0.8154 (mttp) REVERT: C 267 SER cc_start: 0.7728 (p) cc_final: 0.7445 (p) REVERT: C 288 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8015 (mtpt) REVERT: C 318 GLU cc_start: 0.7151 (pp20) cc_final: 0.6673 (pp20) REVERT: C 365 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8168 (mm) outliers start: 11 outliers final: 5 residues processed: 116 average time/residue: 0.4624 time to fit residues: 56.0934 Evaluate side-chains 124 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [50, 3, 51, 35, 20, 37, 0, 52, 44, 30, 56] chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099794 restraints weight = 6976.136| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.18 r_work: 0.3192 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5009 Z= 0.189 Angle : 0.561 8.512 6852 Z= 0.273 Chirality : 0.043 0.126 801 Planarity : 0.004 0.037 846 Dihedral : 5.560 31.688 926 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.44 % Allowed : 13.70 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.34), residues: 580 helix: 0.28 (0.85), residues: 44 sheet: 1.57 (0.30), residues: 262 loop : 0.92 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.015 0.002 TYR B 407 PHE 0.020 0.002 PHE A 57 TRP 0.006 0.001 TRP C 381 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 4988) covalent geometry : angle 0.54348 / 0.27 ( 6795) SS BOND : bond 0.00236 / 0.13 ( 6) SS BOND : angle 0.45867 / 0.26 ( 12) hydrogen bonds : bond 0.03417 / 2.19 ( 195) hydrogen bonds : angle 4.33154 / 2.97 ( 570) link_ALPHA1-3 : bond 0.00903 / 0.61 ( 2) link_ALPHA1-3 : angle 1.51060 / 1.01 ( 6) link_ALPHA1-6 : bond 0.00558 / 0.38 ( 2) link_ALPHA1-6 : angle 1.45699 / 0.91 ( 6) link_BETA1-4 : bond 0.00271 / 0.16 ( 7) link_BETA1-4 : angle 1.84578 / 1.11 ( 21) link_NAG-ASN : bond 0.00204 / 0.13 ( 4) link_NAG-ASN : angle 2.00734 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: B 294 GLU cc_start: 0.7303 (mp0) cc_final: 0.7015 (mp0) REVERT: B 326 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7956 (mttp) REVERT: B 328 LEU cc_start: 0.8334 (mt) cc_final: 0.8101 (mt) REVERT: B 340 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8180 (mttp) REVERT: C 267 SER cc_start: 0.7852 (p) cc_final: 0.7602 (p) REVERT: C 288 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8025 (mtpt) REVERT: C 294 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6706 (mm-30) REVERT: C 318 GLU cc_start: 0.7172 (pp20) cc_final: 0.6719 (pp20) REVERT: C 365 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8152 (mt) REVERT: C 407 TYR cc_start: 0.8764 (m-80) cc_final: 0.8416 (m-80) outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 0.4234 time to fit residues: 56.3737 Evaluate side-chains 132 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [18, 55, 44, 32, 0, 57, 37, 42, 1, 50, 49] chunk 18 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099854 restraints weight = 6937.588| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.20 r_work: 0.3199 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5009 Z= 0.146 Angle : 0.545 8.942 6852 Z= 0.263 Chirality : 0.043 0.128 801 Planarity : 0.004 0.037 846 Dihedral : 5.210 28.212 926 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.44 % Allowed : 14.26 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.34), residues: 580 helix: 0.18 (0.86), residues: 43 sheet: 1.58 (0.30), residues: 257 loop : 0.97 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.011 0.001 TYR B 407 PHE 0.031 0.002 PHE A 57 TRP 0.005 0.001 TRP C 381 HIS 0.003 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4988) covalent geometry : angle 0.52921 / 0.26 ( 6795) SS BOND : bond 0.00163 / 0.09 ( 6) SS BOND : angle 0.38509 / 0.22 ( 12) hydrogen bonds : bond 0.03141 / 2.01 ( 195) hydrogen bonds : angle 4.22298 / 2.90 ( 570) link_ALPHA1-3 : bond 0.00937 / 0.64 ( 2) link_ALPHA1-3 : angle 1.37353 / 0.90 ( 6) link_ALPHA1-6 : bond 0.00567 / 0.39 ( 2) link_ALPHA1-6 : angle 1.42622 / 0.89 ( 6) link_BETA1-4 : bond 0.00288 / 0.18 ( 7) link_BETA1-4 : angle 1.72934 / 1.03 ( 21) link_NAG-ASN : bond 0.00116 / 0.07 ( 4) link_NAG-ASN : angle 1.84054 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: B 326 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7959 (mttp) REVERT: B 328 LEU cc_start: 0.8299 (mt) cc_final: 0.8083 (mt) REVERT: B 340 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8164 (mttp) REVERT: C 267 SER cc_start: 0.7767 (p) cc_final: 0.7516 (p) REVERT: C 288 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8019 (mtpt) REVERT: C 294 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6686 (mm-30) REVERT: C 318 GLU cc_start: 0.7168 (pp20) cc_final: 0.6703 (pp20) REVERT: C 365 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8154 (mm) REVERT: C 407 TYR cc_start: 0.8755 (m-80) cc_final: 0.8413 (m-80) outliers start: 13 outliers final: 7 residues processed: 123 average time/residue: 0.4072 time to fit residues: 52.4817 Evaluate side-chains 128 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [45, 37, 43, 18, 1, 25, 49, 15, 54, 41, 8] chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099775 restraints weight = 7002.535| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.19 r_work: 0.3194 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5009 Z= 0.189 Angle : 0.557 7.753 6852 Z= 0.272 Chirality : 0.043 0.127 801 Planarity : 0.004 0.036 846 Dihedral : 5.231 24.860 926 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.06 % Allowed : 14.82 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.34), residues: 580 helix: -0.03 (0.84), residues: 44 sheet: 1.61 (0.30), residues: 262 loop : 0.89 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.015 0.002 TYR B 407 PHE 0.030 0.002 PHE A 57 TRP 0.006 0.001 TRP A 90 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 4988) covalent geometry : angle 0.53898 / 0.27 ( 6795) SS BOND : bond 0.00234 / 0.13 ( 6) SS BOND : angle 0.41578 / 0.24 ( 12) hydrogen bonds : bond 0.03390 / 2.17 ( 195) hydrogen bonds : angle 4.28621 / 2.94 ( 570) link_ALPHA1-3 : bond 0.00836 / 0.57 ( 2) link_ALPHA1-3 : angle 1.42250 / 0.95 ( 6) link_ALPHA1-6 : bond 0.00446 / 0.31 ( 2) link_ALPHA1-6 : angle 1.47689 / 0.94 ( 6) link_BETA1-4 : bond 0.00271 / 0.16 ( 7) link_BETA1-4 : angle 1.86609 / 1.12 ( 21) link_NAG-ASN : bond 0.00204 / 0.13 ( 4) link_NAG-ASN : angle 2.00048 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: B 294 GLU cc_start: 0.7321 (mp0) cc_final: 0.7037 (mp0) REVERT: B 328 LEU cc_start: 0.8340 (mt) cc_final: 0.8128 (mt) REVERT: B 340 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8175 (mttp) REVERT: C 267 SER cc_start: 0.7855 (p) cc_final: 0.7617 (p) REVERT: C 288 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8027 (mtpt) REVERT: C 294 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6705 (mm-30) REVERT: C 318 GLU cc_start: 0.7194 (pp20) cc_final: 0.6722 (pp20) REVERT: C 365 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 407 TYR cc_start: 0.8761 (m-80) cc_final: 0.8407 (m-80) outliers start: 11 outliers final: 6 residues processed: 120 average time/residue: 0.4391 time to fit residues: 55.0954 Evaluate side-chains 131 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [47, 18, 34, 25, 15, 38, 3, 46, 2, 20, 43] chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100369 restraints weight = 6964.951| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.18 r_work: 0.3198 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5009 Z= 0.148 Angle : 0.549 9.095 6852 Z= 0.267 Chirality : 0.043 0.131 801 Planarity : 0.004 0.036 846 Dihedral : 5.028 22.438 926 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.25 % Allowed : 15.20 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.34), residues: 580 helix: -0.02 (0.85), residues: 43 sheet: 1.61 (0.30), residues: 262 loop : 0.93 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.011 0.001 TYR B 407 PHE 0.031 0.002 PHE A 57 TRP 0.005 0.001 TRP A 90 HIS 0.003 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 4988) covalent geometry : angle 0.53344 / 0.26 ( 6795) SS BOND : bond 0.00165 / 0.10 ( 6) SS BOND : angle 0.37925 / 0.22 ( 12) hydrogen bonds : bond 0.03244 / 2.08 ( 195) hydrogen bonds : angle 4.23816 / 2.92 ( 570) link_ALPHA1-3 : bond 0.00863 / 0.59 ( 2) link_ALPHA1-3 : angle 1.37409 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00474 / 0.33 ( 2) link_ALPHA1-6 : angle 1.44863 / 0.91 ( 6) link_BETA1-4 : bond 0.00283 / 0.18 ( 7) link_BETA1-4 : angle 1.76619 / 1.05 ( 21) link_NAG-ASN : bond 0.00121 / 0.08 ( 4) link_NAG-ASN : angle 1.86843 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: B 328 LEU cc_start: 0.8317 (mt) cc_final: 0.8104 (mt) REVERT: B 414 LYS cc_start: 0.8224 (ttmt) cc_final: 0.8012 (ttmt) REVERT: C 267 SER cc_start: 0.7778 (p) cc_final: 0.7539 (p) REVERT: C 288 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8033 (mtpt) REVERT: C 294 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6679 (mm-30) REVERT: C 318 GLU cc_start: 0.7195 (pp20) cc_final: 0.6734 (pp20) REVERT: C 365 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 407 TYR cc_start: 0.8732 (m-80) cc_final: 0.8458 (m-80) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 0.4742 time to fit residues: 62.8920 Evaluate side-chains 133 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 411 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [57, 36, 46, 15, 23, 55, 3, 44, 54, 43, 47] chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 55 optimal weight: 0.0570 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101013 restraints weight = 6996.529| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.20 r_work: 0.3206 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5009 Z= 0.123 Angle : 0.521 7.254 6852 Z= 0.257 Chirality : 0.042 0.131 801 Planarity : 0.004 0.036 846 Dihedral : 4.779 21.223 926 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.94 % Allowed : 16.32 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.34), residues: 580 helix: -0.06 (0.85), residues: 43 sheet: 1.58 (0.30), residues: 257 loop : 0.99 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.010 0.001 TYR B 407 PHE 0.031 0.002 PHE A 57 TRP 0.006 0.001 TRP C 313 HIS 0.003 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 4988) covalent geometry : angle 0.50589 / 0.25 ( 6795) SS BOND : bond 0.00115 / 0.07 ( 6) SS BOND : angle 0.34078 / 0.20 ( 12) hydrogen bonds : bond 0.03016 / 1.94 ( 195) hydrogen bonds : angle 4.15743 / 2.87 ( 570) link_ALPHA1-3 : bond 0.00839 / 0.57 ( 2) link_ALPHA1-3 : angle 1.34545 / 0.88 ( 6) link_ALPHA1-6 : bond 0.00492 / 0.34 ( 2) link_ALPHA1-6 : angle 1.43555 / 0.90 ( 6) link_BETA1-4 : bond 0.00312 / 0.19 ( 7) link_BETA1-4 : angle 1.70392 / 1.01 ( 21) link_NAG-ASN : bond 0.00085 / 0.05 ( 4) link_NAG-ASN : angle 1.74546 / 0.84 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 328 LEU cc_start: 0.8283 (mt) cc_final: 0.8068 (mt) REVERT: B 414 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7987 (ttmt) REVERT: C 267 SER cc_start: 0.7727 (p) cc_final: 0.7467 (p) REVERT: C 294 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6662 (mm-30) REVERT: C 318 GLU cc_start: 0.7180 (pp20) cc_final: 0.6739 (pp20) REVERT: C 365 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8185 (mt) REVERT: C 407 TYR cc_start: 0.8707 (m-80) cc_final: 0.8444 (m-80) outliers start: 5 outliers final: 3 residues processed: 121 average time/residue: 0.4912 time to fit residues: 61.9872 Evaluate side-chains 124 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: [31, 37, 40, 15, 5, 55, 34, 51, 57, 8, 6] chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099946 restraints weight = 6985.264| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.19 r_work: 0.3186 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5009 Z= 0.208 Angle : 0.577 9.031 6852 Z= 0.281 Chirality : 0.044 0.132 801 Planarity : 0.004 0.035 846 Dihedral : 4.995 22.221 926 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.13 % Allowed : 16.14 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.35), residues: 580 helix: -0.15 (0.85), residues: 43 sheet: 1.60 (0.31), residues: 260 loop : 0.93 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.015 0.002 TYR B 407 PHE 0.032 0.003 PHE A 57 TRP 0.006 0.001 TRP A 90 HIS 0.005 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 ( 4988) covalent geometry : angle 0.56015 / 0.28 ( 6795) SS BOND : bond 0.00247 / 0.14 ( 6) SS BOND : angle 0.42625 / 0.24 ( 12) hydrogen bonds : bond 0.03453 / 2.21 ( 195) hydrogen bonds : angle 4.29977 / 2.96 ( 570) link_ALPHA1-3 : bond 0.00760 / 0.51 ( 2) link_ALPHA1-3 : angle 1.37697 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00390 / 0.27 ( 2) link_ALPHA1-6 : angle 1.49889 / 0.93 ( 6) link_BETA1-4 : bond 0.00280 / 0.17 ( 7) link_BETA1-4 : angle 1.90692 / 1.14 ( 21) link_NAG-ASN : bond 0.00219 / 0.14 ( 4) link_NAG-ASN : angle 2.03310 / 0.97 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1958.46 seconds wall clock time: 34 minutes 7.86 seconds (2047.86 seconds total)