Starting phenix.real_space_refine on Wed Sep 17 07:09:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ele_48146/09_2025/9ele_48146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ele_48146/09_2025/9ele_48146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ele_48146/09_2025/9ele_48146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ele_48146/09_2025/9ele_48146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ele_48146/09_2025/9ele_48146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ele_48146/09_2025/9ele_48146.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4176 2.51 5 N 1066 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6529 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1488 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 11, 'TRANS': 172} Chain: "C" 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: "D" 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: "E" 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: "F" 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: "A" 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: "B" 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 Time building chain proxies: 1.78, per 1000 atoms: 0.27 Number of scatterers: 6529 At special positions: 0 Unit cell: (71.082, 94.776, 111.29, 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 36 16.00 O 1251 8.00 N 1066 7.00 C 4176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Atom "HETATM 6457 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 432 " " NAG B1301 " - " ASN B 354 " " NAG B1302 " - " ASN B 343 " " NAG C 1 " - " ASN A 90 " " NAG D 1 " - " ASN A 322 " " NAG E 1 " - " ASN A 546 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 461.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 60.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.591A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.750A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.536A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.556A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.551A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.527A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.826A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.830A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.801A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 5.203A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.583A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.277A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.011A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 334 hydrogen bonds defined for protein. 933 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: 0.99 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1849 1.34 - 1.46: 1794 1.46 - 1.58: 3013 1.58 - 1.71: 2 1.71 - 1.83: 57 Bond restraints: 6715 Sorted by residual: bond pdb=" CB GLN A 86 " pdb=" CG GLN A 86 " ideal model delta sigma weight residual 1.520 1.609 -0.089 3.00e-02 1.11e+03 8.85e+00 bond pdb=" C ILE A 233 " pdb=" N LYS A 234 " ideal model delta sigma weight residual 1.334 1.370 -0.035 1.26e-02 6.30e+03 7.86e+00 bond pdb=" CB GLU A 171 " pdb=" CG GLU A 171 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.76e+00 bond pdb=" CB GLU A 57 " pdb=" CG GLU A 57 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.29e+00 bond pdb=" CA ASP B 389 " pdb=" CB ASP B 389 " ideal model delta sigma weight residual 1.532 1.568 -0.036 1.74e-02 3.30e+03 4.22e+00 ... (remaining 6710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 8639 2.34 - 4.69: 394 4.69 - 7.03: 71 7.03 - 9.37: 13 9.37 - 11.71: 7 Bond angle restraints: 9124 Sorted by residual: angle pdb=" CB GLU A 171 " pdb=" CG GLU A 171 " pdb=" CD GLU A 171 " ideal model delta sigma weight residual 112.60 122.59 -9.99 1.70e+00 3.46e-01 3.45e+01 angle pdb=" CA GLU A 57 " pdb=" CB GLU A 57 " pdb=" CG GLU A 57 " ideal model delta sigma weight residual 114.10 125.81 -11.71 2.00e+00 2.50e-01 3.43e+01 angle pdb=" CA GLN A 287 " pdb=" CB GLN A 287 " pdb=" CG GLN A 287 " ideal model delta sigma weight residual 114.10 125.61 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" CB GLN A 86 " pdb=" CG GLN A 86 " pdb=" CD GLN A 86 " ideal model delta sigma weight residual 112.60 122.23 -9.63 1.70e+00 3.46e-01 3.21e+01 angle pdb=" CA ASP B 389 " pdb=" CB ASP B 389 " pdb=" CG ASP B 389 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 9119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 3909 21.02 - 42.05: 148 42.05 - 63.07: 48 63.07 - 84.09: 11 84.09 - 105.11: 7 Dihedral angle restraints: 4123 sinusoidal: 1830 harmonic: 2293 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -140.49 54.49 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA ALA B 372 " pdb=" C ALA B 372 " pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 830 0.084 - 0.168: 142 0.168 - 0.252: 9 0.252 - 0.336: 3 0.336 - 0.420: 1 Chirality restraints: 985 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.41e+01 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 982 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " -0.055 2.00e-02 2.50e+03 2.42e-01 7.31e+02 pdb=" CG ASN A 103 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " -0.152 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.433 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.276 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.142 2.00e-02 2.50e+03 1.17e-01 1.71e+02 pdb=" C7 NAG F 2 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.188 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 475 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C LYS A 475 " -0.093 2.00e-02 2.50e+03 pdb=" O LYS A 475 " 0.035 2.00e-02 2.50e+03 pdb=" N LYS A 476 " 0.031 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 14 2.55 - 3.14: 5102 3.14 - 3.73: 10211 3.73 - 4.31: 14676 4.31 - 4.90: 23848 Nonbonded interactions: 53851 Sorted by model distance: nonbonded pdb=" OG SER A 611 " pdb=" CE2 TYR A 613 " model vdw 1.965 3.340 nonbonded pdb=" OG SER A 611 " pdb=" CZ TYR A 613 " model vdw 2.185 3.260 nonbonded pdb=" OG SER A 611 " pdb=" CD2 TYR A 613 " model vdw 2.209 3.340 nonbonded pdb=" CB SER A 611 " pdb=" CE2 TYR A 613 " model vdw 2.209 3.740 nonbonded pdb=" O3 NAG F 1 " pdb=" O5 NAG F 2 " model vdw 2.248 3.040 ... (remaining 53846 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 'C' selection = chain 'D' selection = chain 'F' } 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: 17.330 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.006 0.089 6734 Z= 0.304 Angle : 1.265 25.059 9175 Z= 0.694 Chirality : 0.062 0.420 985 Planarity : 0.010 0.117 1162 Dihedral : 13.420 105.112 2633 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 0.59 (0.28), residues: 776 helix: 0.34 (0.24), residues: 387 sheet: 1.98 (0.68), residues: 45 loop : 0.44 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 460 TYR 0.032 0.003 TYR A 385 PHE 0.029 0.004 PHE B 375 TRP 0.029 0.004 TRP A 203 HIS 0.011 0.003 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 6715) covalent geometry : angle 1.20562 ( 9124) SS BOND : bond 0.00428 ( 6) SS BOND : angle 1.93229 ( 12) hydrogen bonds : bond 0.14975 ( 334) hydrogen bonds : angle 6.91073 ( 933) link_BETA1-4 : bond 0.02111 ( 5) link_BETA1-4 : angle 5.32213 ( 15) link_NAG-ASN : bond 0.00758 ( 8) link_NAG-ASN : angle 6.30635 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7256 (mt-10) REVERT: A 166 GLU cc_start: 0.7100 (tp30) cc_final: 0.6366 (tp30) REVERT: A 185 VAL cc_start: 0.8304 (t) cc_final: 0.7987 (m) REVERT: A 190 MET cc_start: 0.7433 (ttp) cc_final: 0.7211 (ttp) REVERT: A 232 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7113 (mm-30) REVERT: A 259 ILE cc_start: 0.8655 (tp) cc_final: 0.8320 (tt) REVERT: A 298 VAL cc_start: 0.8076 (t) cc_final: 0.7851 (m) REVERT: A 367 ASP cc_start: 0.7564 (m-30) cc_final: 0.7201 (m-30) REVERT: A 470 LYS cc_start: 0.7578 (mtmt) cc_final: 0.6875 (mptt) REVERT: A 578 ASN cc_start: 0.7612 (p0) cc_final: 0.7304 (t0) REVERT: A 597 ASP cc_start: 0.8071 (t70) cc_final: 0.7744 (t70) REVERT: A 600 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7803 (pttm) REVERT: B 357 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7711 (ttt-90) REVERT: B 506 GLN cc_start: 0.8730 (mt0) cc_final: 0.8463 (mt0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0752 time to fit residues: 14.8232 Evaluate side-chains 103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.0000 chunk 74 optimal weight: 0.9990 overall best weight: 0.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 ASN A 373 HIS A 472 GLN A 598 GLN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.143079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114752 restraints weight = 6937.785| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.01 r_work: 0.3156 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6734 Z= 0.161 Angle : 0.666 11.456 9175 Z= 0.330 Chirality : 0.044 0.205 985 Planarity : 0.004 0.029 1162 Dihedral : 6.934 60.843 1118 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.48 % Allowed : 7.87 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.45 (0.29), residues: 776 helix: 1.52 (0.26), residues: 393 sheet: 1.73 (0.74), residues: 44 loop : 0.32 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 559 TYR 0.021 0.002 TYR A 613 PHE 0.021 0.002 PHE A 369 TRP 0.014 0.002 TRP A 478 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6715) covalent geometry : angle 0.62904 ( 9124) SS BOND : bond 0.00597 ( 6) SS BOND : angle 1.14122 ( 12) hydrogen bonds : bond 0.05799 ( 334) hydrogen bonds : angle 5.22164 ( 933) link_BETA1-4 : bond 0.00484 ( 5) link_BETA1-4 : angle 2.83394 ( 15) link_NAG-ASN : bond 0.00359 ( 8) link_NAG-ASN : angle 3.64033 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.240 Fit side-chains REVERT: A 75 GLU cc_start: 0.7764 (mm-30) cc_final: 0.6878 (mt-10) REVERT: A 131 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6928 (ptmm) REVERT: A 166 GLU cc_start: 0.6843 (tp30) cc_final: 0.6242 (tp30) REVERT: A 185 VAL cc_start: 0.8049 (t) cc_final: 0.7582 (m) REVERT: A 190 MET cc_start: 0.7311 (ttp) cc_final: 0.7065 (ttp) REVERT: A 231 GLU cc_start: 0.8017 (tp30) cc_final: 0.7448 (mm-30) REVERT: A 232 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7411 (mm-30) REVERT: A 259 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 325 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7385 (tp40) REVERT: A 367 ASP cc_start: 0.7515 (m-30) cc_final: 0.7123 (m-30) REVERT: A 470 LYS cc_start: 0.7781 (mtmt) cc_final: 0.6996 (mptt) REVERT: A 483 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: A 508 ASN cc_start: 0.7844 (m110) cc_final: 0.7528 (m110) REVERT: A 578 ASN cc_start: 0.7541 (p0) cc_final: 0.7056 (t0) REVERT: A 597 ASP cc_start: 0.8133 (t70) cc_final: 0.7519 (t70) REVERT: A 600 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7347 (pttm) REVERT: B 405 ASN cc_start: 0.8275 (m-40) cc_final: 0.8003 (m110) REVERT: B 420 ASP cc_start: 0.8758 (m-30) cc_final: 0.8497 (m-30) REVERT: B 458 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8490 (mtpt) outliers start: 17 outliers final: 9 residues processed: 106 average time/residue: 0.0782 time to fit residues: 11.2918 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.0070 chunk 55 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.139654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111253 restraints weight = 6900.401| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.99 r_work: 0.3063 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6734 Z= 0.142 Angle : 0.584 8.658 9175 Z= 0.287 Chirality : 0.043 0.197 985 Planarity : 0.004 0.029 1162 Dihedral : 5.332 34.463 1118 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.62 % Allowed : 8.89 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.44 (0.29), residues: 776 helix: 1.61 (0.25), residues: 394 sheet: 0.82 (0.63), residues: 54 loop : 0.29 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 357 TYR 0.020 0.002 TYR A 385 PHE 0.015 0.002 PHE A 369 TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6715) covalent geometry : angle 0.54764 ( 9124) SS BOND : bond 0.00465 ( 6) SS BOND : angle 0.84891 ( 12) hydrogen bonds : bond 0.05209 ( 334) hydrogen bonds : angle 5.01611 ( 933) link_BETA1-4 : bond 0.00450 ( 5) link_BETA1-4 : angle 2.33373 ( 15) link_NAG-ASN : bond 0.00634 ( 8) link_NAG-ASN : angle 3.57444 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.203 Fit side-chains REVERT: A 75 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6857 (mt-10) REVERT: A 166 GLU cc_start: 0.6933 (tp30) cc_final: 0.6370 (tp30) REVERT: A 190 MET cc_start: 0.7469 (ttp) cc_final: 0.7160 (ttp) REVERT: A 231 GLU cc_start: 0.8044 (tp30) cc_final: 0.7493 (mm-30) REVERT: A 232 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7454 (mm-30) REVERT: A 259 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 325 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7297 (tp40) REVERT: A 470 LYS cc_start: 0.7742 (mtmt) cc_final: 0.6973 (mptt) REVERT: A 578 ASN cc_start: 0.7478 (p0) cc_final: 0.7047 (t0) REVERT: A 597 ASP cc_start: 0.8004 (t70) cc_final: 0.7415 (t0) REVERT: A 600 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7348 (pttm) REVERT: B 357 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8105 (ttp80) REVERT: B 391 CYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6845 (m) REVERT: B 405 ASN cc_start: 0.8366 (m-40) cc_final: 0.8018 (m110) REVERT: B 420 ASP cc_start: 0.8750 (m-30) cc_final: 0.8274 (m-30) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.0827 time to fit residues: 10.8325 Evaluate side-chains 93 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.130179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100947 restraints weight = 7146.598| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.06 r_work: 0.2899 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6734 Z= 0.211 Angle : 0.614 7.573 9175 Z= 0.304 Chirality : 0.044 0.174 985 Planarity : 0.004 0.037 1162 Dihedral : 4.972 35.710 1118 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.21 % Allowed : 9.91 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.18 (0.29), residues: 776 helix: 1.53 (0.26), residues: 390 sheet: 0.28 (0.60), residues: 54 loop : 0.07 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.022 0.002 TYR A 385 PHE 0.021 0.002 PHE A 369 TRP 0.015 0.002 TRP B 436 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 6715) covalent geometry : angle 0.58437 ( 9124) SS BOND : bond 0.00642 ( 6) SS BOND : angle 1.01998 ( 12) hydrogen bonds : bond 0.05550 ( 334) hydrogen bonds : angle 4.93830 ( 933) link_BETA1-4 : bond 0.00509 ( 5) link_BETA1-4 : angle 2.05720 ( 15) link_NAG-ASN : bond 0.00393 ( 8) link_NAG-ASN : angle 3.35174 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.247 Fit side-chains REVERT: A 75 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6839 (mt-10) REVERT: A 131 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6735 (ptmm) REVERT: A 166 GLU cc_start: 0.6965 (tp30) cc_final: 0.6331 (tp30) REVERT: A 190 MET cc_start: 0.7502 (ttp) cc_final: 0.7201 (ttp) REVERT: A 231 GLU cc_start: 0.8092 (tp30) cc_final: 0.7496 (mm-30) REVERT: A 232 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7594 (mm-30) REVERT: A 259 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8178 (tt) REVERT: A 470 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7103 (mptt) REVERT: A 557 MET cc_start: 0.8779 (tmm) cc_final: 0.8541 (ttp) REVERT: A 577 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7468 (ttpp) REVERT: A 578 ASN cc_start: 0.7564 (p0) cc_final: 0.7075 (t0) REVERT: A 597 ASP cc_start: 0.8063 (t70) cc_final: 0.7501 (t0) REVERT: A 600 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7258 (pttm) REVERT: B 357 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8186 (ttp80) REVERT: B 391 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6861 (m) REVERT: B 405 ASN cc_start: 0.8517 (m-40) cc_final: 0.8132 (m110) REVERT: B 420 ASP cc_start: 0.8916 (m-30) cc_final: 0.8443 (m-30) outliers start: 22 outliers final: 15 residues processed: 99 average time/residue: 0.0840 time to fit residues: 11.1440 Evaluate side-chains 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 74 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 55 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.0030 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN A 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105264 restraints weight = 7084.145| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.05 r_work: 0.2958 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6734 Z= 0.135 Angle : 0.550 7.169 9175 Z= 0.269 Chirality : 0.041 0.178 985 Planarity : 0.004 0.028 1162 Dihedral : 4.752 33.769 1118 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.77 % Allowed : 11.08 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.23 (0.29), residues: 776 helix: 1.59 (0.26), residues: 392 sheet: 0.02 (0.60), residues: 54 loop : 0.12 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.017 0.001 TYR A 385 PHE 0.015 0.001 PHE A 369 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6715) covalent geometry : angle 0.52102 ( 9124) SS BOND : bond 0.00491 ( 6) SS BOND : angle 0.72820 ( 12) hydrogen bonds : bond 0.04935 ( 334) hydrogen bonds : angle 4.87899 ( 933) link_BETA1-4 : bond 0.00515 ( 5) link_BETA1-4 : angle 1.98778 ( 15) link_NAG-ASN : bond 0.00787 ( 8) link_NAG-ASN : angle 3.14563 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.247 Fit side-chains REVERT: A 75 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6859 (mt-10) REVERT: A 166 GLU cc_start: 0.6940 (tp30) cc_final: 0.6323 (tp30) REVERT: A 190 MET cc_start: 0.7467 (ttp) cc_final: 0.7183 (ttp) REVERT: A 231 GLU cc_start: 0.8094 (tp30) cc_final: 0.7496 (mm-30) REVERT: A 232 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7522 (mm-30) REVERT: A 259 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 269 ASP cc_start: 0.8313 (t0) cc_final: 0.7907 (t0) REVERT: A 470 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7108 (mptt) REVERT: A 480 MET cc_start: 0.8107 (mtm) cc_final: 0.7858 (mtm) REVERT: A 557 MET cc_start: 0.8781 (tmm) cc_final: 0.8534 (ttp) REVERT: A 577 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7493 (ttpp) REVERT: A 578 ASN cc_start: 0.7476 (p0) cc_final: 0.7010 (t0) REVERT: A 597 ASP cc_start: 0.8016 (t70) cc_final: 0.7483 (t0) REVERT: A 600 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7262 (pttm) REVERT: B 391 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6866 (m) REVERT: B 405 ASN cc_start: 0.8506 (m-40) cc_final: 0.8115 (m110) REVERT: B 420 ASP cc_start: 0.8876 (m-30) cc_final: 0.8380 (m-30) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 0.0795 time to fit residues: 10.0274 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101068 restraints weight = 7180.724| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.06 r_work: 0.2897 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6734 Z= 0.191 Angle : 0.577 6.836 9175 Z= 0.283 Chirality : 0.042 0.170 985 Planarity : 0.004 0.030 1162 Dihedral : 4.740 35.112 1118 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.06 % Allowed : 11.08 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.06 (0.29), residues: 776 helix: 1.49 (0.26), residues: 392 sheet: -0.24 (0.59), residues: 54 loop : 0.01 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.019 0.002 TYR A 385 PHE 0.019 0.002 PHE A 369 TRP 0.012 0.001 TRP B 436 HIS 0.007 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 6715) covalent geometry : angle 0.54824 ( 9124) SS BOND : bond 0.00612 ( 6) SS BOND : angle 0.86045 ( 12) hydrogen bonds : bond 0.05232 ( 334) hydrogen bonds : angle 4.86816 ( 933) link_BETA1-4 : bond 0.00478 ( 5) link_BETA1-4 : angle 1.96426 ( 15) link_NAG-ASN : bond 0.00440 ( 8) link_NAG-ASN : angle 3.22870 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6857 (mt-10) REVERT: A 87 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7066 (pm20) REVERT: A 91 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7361 (mt) REVERT: A 166 GLU cc_start: 0.6913 (tp30) cc_final: 0.6260 (tp30) REVERT: A 190 MET cc_start: 0.7488 (ttp) cc_final: 0.7192 (ttp) REVERT: A 231 GLU cc_start: 0.8102 (tp30) cc_final: 0.7473 (mm-30) REVERT: A 232 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7572 (mm-30) REVERT: A 259 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8124 (tt) REVERT: A 269 ASP cc_start: 0.8339 (t0) cc_final: 0.7952 (t0) REVERT: A 470 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7198 (mptt) REVERT: A 480 MET cc_start: 0.8152 (mtm) cc_final: 0.7910 (mtm) REVERT: A 522 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8733 (pt0) REVERT: A 557 MET cc_start: 0.8760 (tmm) cc_final: 0.8531 (ttp) REVERT: A 577 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7444 (ttpp) REVERT: A 578 ASN cc_start: 0.7494 (p0) cc_final: 0.7031 (t0) REVERT: A 597 ASP cc_start: 0.8076 (t70) cc_final: 0.7557 (t0) REVERT: A 600 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7254 (pttm) REVERT: B 391 CYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6879 (m) REVERT: B 420 ASP cc_start: 0.8940 (m-30) cc_final: 0.8406 (m-30) outliers start: 21 outliers final: 16 residues processed: 95 average time/residue: 0.0850 time to fit residues: 11.0205 Evaluate side-chains 104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 76 optimal weight: 0.0670 chunk 54 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105740 restraints weight = 7062.006| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.04 r_work: 0.3014 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6734 Z= 0.119 Angle : 0.529 6.874 9175 Z= 0.258 Chirality : 0.040 0.174 985 Planarity : 0.003 0.028 1162 Dihedral : 4.566 32.648 1118 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.92 % Allowed : 11.66 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.21 (0.29), residues: 776 helix: 1.71 (0.26), residues: 385 sheet: -0.23 (0.59), residues: 54 loop : 0.00 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.015 0.001 TYR A 385 PHE 0.014 0.001 PHE A 369 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6715) covalent geometry : angle 0.50081 ( 9124) SS BOND : bond 0.00463 ( 6) SS BOND : angle 0.62779 ( 12) hydrogen bonds : bond 0.04672 ( 334) hydrogen bonds : angle 4.82221 ( 933) link_BETA1-4 : bond 0.00480 ( 5) link_BETA1-4 : angle 1.87978 ( 15) link_NAG-ASN : bond 0.00697 ( 8) link_NAG-ASN : angle 3.01474 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6905 (tt0) REVERT: A 87 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6974 (pm20) REVERT: A 91 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7394 (mt) REVERT: A 166 GLU cc_start: 0.6916 (tp30) cc_final: 0.6290 (tp30) REVERT: A 190 MET cc_start: 0.7450 (ttp) cc_final: 0.7177 (ttp) REVERT: A 231 GLU cc_start: 0.8070 (tp30) cc_final: 0.7461 (mm-30) REVERT: A 232 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7506 (mm-30) REVERT: A 259 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 269 ASP cc_start: 0.8314 (t0) cc_final: 0.7904 (t0) REVERT: A 470 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7263 (mptt) REVERT: A 480 MET cc_start: 0.8067 (mtm) cc_final: 0.7838 (mtm) REVERT: A 577 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7534 (ttpp) REVERT: A 578 ASN cc_start: 0.7390 (p0) cc_final: 0.6964 (t0) REVERT: A 597 ASP cc_start: 0.8008 (t70) cc_final: 0.7495 (t0) REVERT: A 600 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7247 (pttm) REVERT: B 391 CYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6915 (m) REVERT: B 420 ASP cc_start: 0.8860 (m-30) cc_final: 0.8304 (m-30) outliers start: 20 outliers final: 14 residues processed: 97 average time/residue: 0.0808 time to fit residues: 10.9007 Evaluate side-chains 102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.100280 restraints weight = 7217.775| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.06 r_work: 0.2864 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6734 Z= 0.194 Angle : 0.584 7.117 9175 Z= 0.285 Chirality : 0.043 0.165 985 Planarity : 0.004 0.031 1162 Dihedral : 4.704 35.110 1118 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.35 % Allowed : 11.22 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.00 (0.29), residues: 776 helix: 1.49 (0.26), residues: 392 sheet: -0.45 (0.59), residues: 54 loop : -0.05 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.020 0.002 TYR A 385 PHE 0.019 0.002 PHE A 369 TRP 0.012 0.001 TRP A 477 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 6715) covalent geometry : angle 0.55588 ( 9124) SS BOND : bond 0.00616 ( 6) SS BOND : angle 0.84896 ( 12) hydrogen bonds : bond 0.05278 ( 334) hydrogen bonds : angle 4.85512 ( 933) link_BETA1-4 : bond 0.00407 ( 5) link_BETA1-4 : angle 1.92937 ( 15) link_NAG-ASN : bond 0.00441 ( 8) link_NAG-ASN : angle 3.16442 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.244 Fit side-chains REVERT: A 75 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6941 (tt0) REVERT: A 87 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6880 (pm20) REVERT: A 166 GLU cc_start: 0.6946 (tp30) cc_final: 0.6286 (tp30) REVERT: A 190 MET cc_start: 0.7533 (ttp) cc_final: 0.7237 (ttp) REVERT: A 231 GLU cc_start: 0.8108 (tp30) cc_final: 0.7482 (mm-30) REVERT: A 232 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7573 (mm-30) REVERT: A 259 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 470 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7362 (mptt) REVERT: A 522 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8739 (pt0) REVERT: A 557 MET cc_start: 0.8790 (tmm) cc_final: 0.8555 (ttp) REVERT: A 577 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7506 (ttpp) REVERT: A 578 ASN cc_start: 0.7499 (p0) cc_final: 0.7069 (t0) REVERT: A 597 ASP cc_start: 0.8087 (t70) cc_final: 0.7584 (t0) REVERT: A 600 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7262 (pttm) REVERT: B 391 CYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6878 (m) REVERT: B 405 ASN cc_start: 0.8591 (m-40) cc_final: 0.8036 (m-40) REVERT: B 420 ASP cc_start: 0.8976 (m-30) cc_final: 0.8438 (m-30) outliers start: 23 outliers final: 17 residues processed: 95 average time/residue: 0.0754 time to fit residues: 9.7814 Evaluate side-chains 104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.129822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.100469 restraints weight = 7274.718| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.07 r_work: 0.2886 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6734 Z= 0.174 Angle : 0.567 6.711 9175 Z= 0.276 Chirality : 0.042 0.162 985 Planarity : 0.004 0.030 1162 Dihedral : 4.663 34.599 1118 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.06 % Allowed : 11.37 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 0.99 (0.29), residues: 776 helix: 1.58 (0.26), residues: 385 sheet: -0.55 (0.60), residues: 54 loop : -0.13 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.018 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6715) covalent geometry : angle 0.53893 ( 9124) SS BOND : bond 0.00590 ( 6) SS BOND : angle 0.77756 ( 12) hydrogen bonds : bond 0.05108 ( 334) hydrogen bonds : angle 4.84998 ( 933) link_BETA1-4 : bond 0.00410 ( 5) link_BETA1-4 : angle 1.89697 ( 15) link_NAG-ASN : bond 0.00417 ( 8) link_NAG-ASN : angle 3.16163 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.294 Fit side-chains REVERT: A 75 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6947 (tt0) REVERT: A 87 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6908 (pm20) REVERT: A 126 ILE cc_start: 0.7777 (mt) cc_final: 0.7529 (mt) REVERT: A 166 GLU cc_start: 0.6925 (tp30) cc_final: 0.6283 (tp30) REVERT: A 190 MET cc_start: 0.7511 (ttp) cc_final: 0.7224 (ttp) REVERT: A 231 GLU cc_start: 0.8104 (tp30) cc_final: 0.7468 (mm-30) REVERT: A 232 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7551 (mm-30) REVERT: A 259 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 470 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7420 (mptt) REVERT: A 522 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8708 (pt0) REVERT: A 557 MET cc_start: 0.8802 (tmm) cc_final: 0.8565 (ttp) REVERT: A 577 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7491 (ttpp) REVERT: A 578 ASN cc_start: 0.7460 (p0) cc_final: 0.7032 (t0) REVERT: A 597 ASP cc_start: 0.8089 (t70) cc_final: 0.7633 (t0) REVERT: A 600 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7293 (pttm) REVERT: B 391 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6925 (m) REVERT: B 420 ASP cc_start: 0.8957 (m-30) cc_final: 0.8387 (m-30) outliers start: 21 outliers final: 17 residues processed: 93 average time/residue: 0.0815 time to fit residues: 10.4164 Evaluate side-chains 102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 59 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.129225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100694 restraints weight = 7132.129| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.95 r_work: 0.2936 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6734 Z= 0.154 Angle : 0.554 6.690 9175 Z= 0.269 Chirality : 0.041 0.164 985 Planarity : 0.004 0.029 1162 Dihedral : 4.581 33.925 1118 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.06 % Allowed : 11.66 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.04 (0.29), residues: 776 helix: 1.61 (0.26), residues: 385 sheet: -0.00 (0.64), residues: 44 loop : -0.20 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.017 0.001 TYR A 385 PHE 0.016 0.001 PHE A 369 TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6715) covalent geometry : angle 0.52594 ( 9124) SS BOND : bond 0.00549 ( 6) SS BOND : angle 0.71245 ( 12) hydrogen bonds : bond 0.04938 ( 334) hydrogen bonds : angle 4.82361 ( 933) link_BETA1-4 : bond 0.00449 ( 5) link_BETA1-4 : angle 1.86994 ( 15) link_NAG-ASN : bond 0.00419 ( 8) link_NAG-ASN : angle 3.11571 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.281 Fit side-chains REVERT: A 75 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7030 (tt0) REVERT: A 87 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6914 (pm20) REVERT: A 123 MET cc_start: 0.6711 (mtt) cc_final: 0.6467 (mtt) REVERT: A 126 ILE cc_start: 0.7853 (mt) cc_final: 0.7568 (mt) REVERT: A 166 GLU cc_start: 0.7000 (tp30) cc_final: 0.6358 (tp30) REVERT: A 190 MET cc_start: 0.7555 (ttp) cc_final: 0.7269 (ttp) REVERT: A 231 GLU cc_start: 0.8091 (tp30) cc_final: 0.7479 (mm-30) REVERT: A 232 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7565 (mm-30) REVERT: A 259 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8149 (tt) REVERT: A 470 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7496 (mptt) REVERT: A 522 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8735 (pt0) REVERT: A 557 MET cc_start: 0.8832 (tmm) cc_final: 0.8561 (ttp) REVERT: A 577 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7507 (ttpp) REVERT: A 578 ASN cc_start: 0.7441 (p0) cc_final: 0.7047 (t0) REVERT: A 597 ASP cc_start: 0.8122 (t70) cc_final: 0.7684 (t0) REVERT: A 600 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7350 (pttm) REVERT: B 391 CYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6936 (m) REVERT: B 420 ASP cc_start: 0.8927 (m-30) cc_final: 0.8368 (m-30) outliers start: 21 outliers final: 17 residues processed: 93 average time/residue: 0.0804 time to fit residues: 10.2600 Evaluate side-chains 103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 55 optimal weight: 0.0770 chunk 6 optimal weight: 0.0970 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107616 restraints weight = 7044.495| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.04 r_work: 0.2962 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6734 Z= 0.116 Angle : 0.520 6.607 9175 Z= 0.253 Chirality : 0.040 0.166 985 Planarity : 0.003 0.028 1162 Dihedral : 4.387 31.682 1118 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.06 % Allowed : 11.37 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: 1.18 (0.30), residues: 776 helix: 1.70 (0.26), residues: 385 sheet: 0.08 (0.65), residues: 44 loop : -0.10 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.016 0.001 TYR A 50 PHE 0.014 0.001 PHE A 369 TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6715) covalent geometry : angle 0.49233 ( 9124) SS BOND : bond 0.00467 ( 6) SS BOND : angle 0.62635 ( 12) hydrogen bonds : bond 0.04556 ( 334) hydrogen bonds : angle 4.75979 ( 933) link_BETA1-4 : bond 0.00473 ( 5) link_BETA1-4 : angle 1.80462 ( 15) link_NAG-ASN : bond 0.00418 ( 8) link_NAG-ASN : angle 2.99633 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.69 seconds wall clock time: 37 minutes 43.54 seconds (2263.54 seconds total)