Starting phenix.real_space_refine on Thu Jun 5 17:26:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ele_48146/06_2025/9ele_48146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ele_48146/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ele_48146/06_2025/9ele_48146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ele_48146/06_2025/9ele_48146.map" model { file = "/net/cci-nas-00/data/ceres_data/9ele_48146/06_2025/9ele_48146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ele_48146/06_2025/9ele_48146.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.20, per 1000 atoms: 1.72 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.72 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: 1.80 Time building geometry restraints manager: 2.44 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: 732.190 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 29.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 765.010 ------------------------------------------------------------------------------- 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 : 2.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.004 TRP A 203 HIS 0.011 0.003 HIS B 505 PHE 0.029 0.004 PHE B 375 TYR 0.032 0.003 TYR A 385 ARG 0.015 0.002 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 8) link_NAG-ASN : angle 6.30635 ( 24) link_BETA1-4 : bond 0.02111 ( 5) link_BETA1-4 : angle 5.32213 ( 15) hydrogen bonds : bond 0.14975 ( 334) hydrogen bonds : angle 6.91073 ( 933) SS BOND : bond 0.00428 ( 6) SS BOND : angle 1.93229 ( 12) covalent geometry : bond 0.00645 ( 6715) covalent geometry : angle 1.20562 ( 9124) *********************** 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 : 0.831 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: 0.2054 time to fit residues: 40.0417 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 : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 241 HIS A 373 HIS A 472 GLN A 598 GLN B 448 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112236 restraints weight = 6862.182| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.03 r_work: 0.3147 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6734 Z= 0.183 Angle : 0.683 11.893 9175 Z= 0.339 Chirality : 0.045 0.201 985 Planarity : 0.004 0.033 1162 Dihedral : 6.939 60.217 1118 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.62 % Allowed : 8.16 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.29), residues: 776 helix: 1.43 (0.26), residues: 393 sheet: 1.20 (0.67), residues: 54 loop : 0.32 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 478 HIS 0.006 0.001 HIS A 228 PHE 0.023 0.002 PHE A 369 TYR 0.021 0.002 TYR A 385 ARG 0.005 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 8) link_NAG-ASN : angle 3.72879 ( 24) link_BETA1-4 : bond 0.00662 ( 5) link_BETA1-4 : angle 2.76240 ( 15) hydrogen bonds : bond 0.05903 ( 334) hydrogen bonds : angle 5.23964 ( 933) SS BOND : bond 0.00640 ( 6) SS BOND : angle 1.18600 ( 12) covalent geometry : bond 0.00418 ( 6715) covalent geometry : angle 0.64708 ( 9124) *********************** 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: 18 poor density : 93 time to evaluate : 0.696 Fit side-chains REVERT: A 56 GLU cc_start: 0.7742 (tp30) cc_final: 0.7483 (tp30) REVERT: A 75 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6908 (mt-10) REVERT: A 131 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7019 (ptmm) REVERT: A 166 GLU cc_start: 0.6909 (tp30) cc_final: 0.6293 (tp30) REVERT: A 190 MET cc_start: 0.7393 (ttp) cc_final: 0.7133 (ttp) REVERT: A 231 GLU cc_start: 0.8042 (tp30) cc_final: 0.7473 (mm-30) REVERT: A 232 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7451 (mm-30) REVERT: A 259 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8144 (tt) REVERT: A 325 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7638 (tp40) REVERT: A 367 ASP cc_start: 0.7567 (m-30) cc_final: 0.7177 (m-30) REVERT: A 470 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7041 (mptt) REVERT: A 483 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: A 508 ASN cc_start: 0.7851 (m110) cc_final: 0.7575 (m110) REVERT: A 578 ASN cc_start: 0.7578 (p0) cc_final: 0.7110 (t0) REVERT: A 597 ASP cc_start: 0.8095 (t70) cc_final: 0.7493 (t70) REVERT: A 600 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7394 (pttm) REVERT: B 364 ASP cc_start: 0.7478 (p0) cc_final: 0.7265 (p0) REVERT: B 405 ASN cc_start: 0.8351 (m-40) cc_final: 0.8010 (m110) REVERT: B 420 ASP cc_start: 0.8845 (m-30) cc_final: 0.8551 (m-30) REVERT: B 458 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8525 (mtpt) outliers start: 18 outliers final: 9 residues processed: 105 average time/residue: 0.1910 time to fit residues: 26.9507 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.140412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112187 restraints weight = 6937.187| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.99 r_work: 0.3047 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6734 Z= 0.130 Angle : 0.577 9.057 9175 Z= 0.282 Chirality : 0.042 0.202 985 Planarity : 0.004 0.030 1162 Dihedral : 5.440 33.701 1118 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.92 % Allowed : 8.31 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 776 helix: 1.60 (0.25), residues: 394 sheet: 0.83 (0.64), residues: 54 loop : 0.31 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 PHE 0.014 0.001 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00959 ( 8) link_NAG-ASN : angle 3.54403 ( 24) link_BETA1-4 : bond 0.00517 ( 5) link_BETA1-4 : angle 2.41052 ( 15) hydrogen bonds : bond 0.05143 ( 334) hydrogen bonds : angle 5.01148 ( 933) SS BOND : bond 0.00446 ( 6) SS BOND : angle 0.82732 ( 12) covalent geometry : bond 0.00279 ( 6715) covalent geometry : angle 0.54002 ( 9124) *********************** 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: 20 poor density : 85 time to evaluate : 0.720 Fit side-chains REVERT: A 75 GLU cc_start: 0.7715 (mm-30) cc_final: 0.6871 (mt-10) REVERT: A 166 GLU cc_start: 0.6930 (tp30) cc_final: 0.6371 (tp30) REVERT: A 190 MET cc_start: 0.7432 (ttp) cc_final: 0.7153 (ttp) REVERT: A 231 GLU cc_start: 0.8051 (tp30) cc_final: 0.7486 (mm-30) REVERT: A 232 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7472 (mm-30) REVERT: A 259 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8079 (tt) REVERT: A 325 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7359 (tp40) REVERT: A 367 ASP cc_start: 0.7531 (m-30) cc_final: 0.7133 (m-30) REVERT: A 470 LYS cc_start: 0.7749 (mtmt) cc_final: 0.6993 (mptt) REVERT: A 577 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7305 (ttpp) REVERT: A 578 ASN cc_start: 0.7504 (p0) cc_final: 0.7045 (t0) REVERT: A 597 ASP cc_start: 0.8016 (t70) cc_final: 0.7446 (t0) REVERT: A 600 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7378 (pttm) REVERT: B 391 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6817 (m) REVERT: B 405 ASN cc_start: 0.8367 (m-40) cc_final: 0.8024 (m110) REVERT: B 420 ASP cc_start: 0.8761 (m-30) cc_final: 0.8331 (m-30) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.1913 time to fit residues: 24.7266 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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 611 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.106758 restraints weight = 7080.373| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.06 r_work: 0.2955 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6734 Z= 0.147 Angle : 0.552 7.843 9175 Z= 0.272 Chirality : 0.042 0.188 985 Planarity : 0.004 0.029 1162 Dihedral : 4.771 33.447 1118 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.92 % Allowed : 10.06 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 776 helix: 1.65 (0.26), residues: 391 sheet: 0.59 (0.61), residues: 54 loop : 0.19 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS A 535 PHE 0.018 0.002 PHE A 369 TYR 0.020 0.002 TYR A 385 ARG 0.004 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 8) link_NAG-ASN : angle 3.20161 ( 24) link_BETA1-4 : bond 0.00634 ( 5) link_BETA1-4 : angle 2.07856 ( 15) hydrogen bonds : bond 0.05001 ( 334) hydrogen bonds : angle 4.86565 ( 933) SS BOND : bond 0.00493 ( 6) SS BOND : angle 0.82566 ( 12) covalent geometry : bond 0.00339 ( 6715) covalent geometry : angle 0.52134 ( 9124) *********************** 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 102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.770 Fit side-chains REVERT: A 75 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6854 (mt-10) REVERT: A 166 GLU cc_start: 0.6984 (tp30) cc_final: 0.6380 (tp30) REVERT: A 190 MET cc_start: 0.7439 (ttp) cc_final: 0.7152 (ttp) REVERT: A 231 GLU cc_start: 0.8073 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 232 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7486 (mm-30) REVERT: A 259 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 470 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7000 (mptt) REVERT: A 577 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7326 (ttpp) REVERT: A 597 ASP cc_start: 0.8024 (t70) cc_final: 0.7426 (t0) REVERT: A 600 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7302 (pttm) REVERT: B 391 CYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6839 (m) REVERT: B 420 ASP cc_start: 0.8829 (m-30) cc_final: 0.8348 (m-30) outliers start: 20 outliers final: 12 residues processed: 93 average time/residue: 0.2406 time to fit residues: 30.3069 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.5980 chunk 68 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109739 restraints weight = 6986.328| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.01 r_work: 0.3017 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6734 Z= 0.123 Angle : 0.528 7.430 9175 Z= 0.258 Chirality : 0.041 0.182 985 Planarity : 0.004 0.028 1162 Dihedral : 4.464 32.376 1118 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.19 % Allowed : 10.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 776 helix: 1.77 (0.26), residues: 389 sheet: 0.32 (0.61), residues: 54 loop : 0.20 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.008 0.001 HIS A 535 PHE 0.015 0.001 PHE A 369 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 8) link_NAG-ASN : angle 3.14466 ( 24) link_BETA1-4 : bond 0.00501 ( 5) link_BETA1-4 : angle 1.92386 ( 15) hydrogen bonds : bond 0.04683 ( 334) hydrogen bonds : angle 4.78053 ( 933) SS BOND : bond 0.00466 ( 6) SS BOND : angle 0.71705 ( 12) covalent geometry : bond 0.00275 ( 6715) covalent geometry : angle 0.49728 ( 9124) *********************** 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 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.174 Fit side-chains REVERT: A 75 GLU cc_start: 0.7692 (mm-30) cc_final: 0.6843 (mt-10) REVERT: A 166 GLU cc_start: 0.7000 (tp30) cc_final: 0.6370 (tp30) REVERT: A 190 MET cc_start: 0.7437 (ttp) cc_final: 0.7155 (ttp) REVERT: A 231 GLU cc_start: 0.8046 (tp30) cc_final: 0.7462 (mm-30) REVERT: A 232 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7451 (mm-30) REVERT: A 259 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 470 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7072 (mptt) REVERT: A 480 MET cc_start: 0.8064 (mtm) cc_final: 0.7809 (mtm) REVERT: A 522 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8672 (pt0) REVERT: A 577 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7452 (ttpp) REVERT: A 578 ASN cc_start: 0.7391 (p0) cc_final: 0.6961 (t0) REVERT: A 597 ASP cc_start: 0.7980 (t70) cc_final: 0.7436 (t0) REVERT: A 600 LYS cc_start: 0.8049 (mtpt) cc_final: 0.7325 (pttm) REVERT: B 391 CYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6843 (m) REVERT: B 420 ASP cc_start: 0.8788 (m-30) cc_final: 0.8288 (m-30) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 0.2671 time to fit residues: 32.2809 Evaluate side-chains 89 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 356 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 66 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.136372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107426 restraints weight = 6940.456| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.04 r_work: 0.3137 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6734 Z= 0.123 Angle : 0.524 6.924 9175 Z= 0.256 Chirality : 0.041 0.180 985 Planarity : 0.003 0.027 1162 Dihedral : 4.385 31.834 1118 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.21 % Allowed : 10.20 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 776 helix: 1.92 (0.26), residues: 377 sheet: 0.19 (0.59), residues: 54 loop : 0.18 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 PHE 0.015 0.001 PHE A 369 TYR 0.017 0.001 TYR A 385 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 8) link_NAG-ASN : angle 3.07153 ( 24) link_BETA1-4 : bond 0.00470 ( 5) link_BETA1-4 : angle 1.85911 ( 15) hydrogen bonds : bond 0.04646 ( 334) hydrogen bonds : angle 4.73980 ( 933) SS BOND : bond 0.00462 ( 6) SS BOND : angle 0.71842 ( 12) covalent geometry : bond 0.00276 ( 6715) covalent geometry : angle 0.49498 ( 9124) *********************** 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 103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.774 Fit side-chains REVERT: A 75 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6797 (mt-10) REVERT: A 87 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6875 (pm20) REVERT: A 166 GLU cc_start: 0.6940 (tp30) cc_final: 0.6317 (tp30) REVERT: A 190 MET cc_start: 0.7405 (ttp) cc_final: 0.7125 (ttp) REVERT: A 231 GLU cc_start: 0.8043 (tp30) cc_final: 0.7445 (mm-30) REVERT: A 232 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7413 (mm-30) REVERT: A 259 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 470 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7048 (mptt) REVERT: A 480 MET cc_start: 0.8025 (mtm) cc_final: 0.7785 (mtm) REVERT: A 557 MET cc_start: 0.8765 (tmm) cc_final: 0.8125 (ttp) REVERT: A 577 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7447 (ttpp) REVERT: A 578 ASN cc_start: 0.7352 (p0) cc_final: 0.6949 (t0) REVERT: A 597 ASP cc_start: 0.7949 (t70) cc_final: 0.7403 (t0) REVERT: A 600 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7260 (pttm) REVERT: B 391 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6958 (m) REVERT: B 420 ASP cc_start: 0.8805 (m-30) cc_final: 0.8287 (m-30) outliers start: 22 outliers final: 14 residues processed: 94 average time/residue: 0.2487 time to fit residues: 32.5425 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 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 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 32 optimal weight: 0.0050 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107039 restraints weight = 6955.657| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.03 r_work: 0.3131 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6734 Z= 0.126 Angle : 0.525 7.144 9175 Z= 0.256 Chirality : 0.041 0.177 985 Planarity : 0.003 0.027 1162 Dihedral : 4.430 31.455 1118 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.62 % Allowed : 11.08 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 776 helix: 1.94 (0.26), residues: 377 sheet: 0.13 (0.59), residues: 54 loop : 0.14 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS A 535 PHE 0.015 0.001 PHE A 369 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 8) link_NAG-ASN : angle 3.02188 ( 24) link_BETA1-4 : bond 0.00471 ( 5) link_BETA1-4 : angle 1.82424 ( 15) hydrogen bonds : bond 0.04638 ( 334) hydrogen bonds : angle 4.76350 ( 933) SS BOND : bond 0.00466 ( 6) SS BOND : angle 0.68078 ( 12) covalent geometry : bond 0.00285 ( 6715) covalent geometry : angle 0.49694 ( 9124) *********************** 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 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.679 Fit side-chains REVERT: A 75 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6894 (tt0) REVERT: A 87 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6903 (pm20) REVERT: A 166 GLU cc_start: 0.6916 (tp30) cc_final: 0.6294 (tp30) REVERT: A 190 MET cc_start: 0.7404 (ttp) cc_final: 0.7112 (ttp) REVERT: A 231 GLU cc_start: 0.8036 (tp30) cc_final: 0.7434 (mm-30) REVERT: A 232 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7449 (mm-30) REVERT: A 259 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8055 (tt) REVERT: A 470 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7094 (mptt) REVERT: A 480 MET cc_start: 0.8008 (mtm) cc_final: 0.7776 (mtm) REVERT: A 557 MET cc_start: 0.8756 (tmm) cc_final: 0.8133 (ttp) REVERT: A 577 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7454 (ttpp) REVERT: A 578 ASN cc_start: 0.7331 (p0) cc_final: 0.6941 (t0) REVERT: A 597 ASP cc_start: 0.7980 (t70) cc_final: 0.7497 (t0) REVERT: A 600 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7282 (pttm) REVERT: B 391 CYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7054 (m) REVERT: B 420 ASP cc_start: 0.8796 (m-30) cc_final: 0.8284 (m-30) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.2012 time to fit residues: 25.7523 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 391 CYS 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 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.130471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.101110 restraints weight = 7099.462| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.04 r_work: 0.2974 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6734 Z= 0.192 Angle : 0.583 6.683 9175 Z= 0.285 Chirality : 0.043 0.166 985 Planarity : 0.004 0.029 1162 Dihedral : 4.618 33.822 1118 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.62 % Allowed : 11.37 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 776 helix: 1.58 (0.26), residues: 392 sheet: -0.18 (0.58), residues: 54 loop : -0.06 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS A 535 PHE 0.019 0.002 PHE A 369 TYR 0.020 0.002 TYR A 385 ARG 0.003 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 8) link_NAG-ASN : angle 3.17577 ( 24) link_BETA1-4 : bond 0.00429 ( 5) link_BETA1-4 : angle 1.88189 ( 15) hydrogen bonds : bond 0.05223 ( 334) hydrogen bonds : angle 4.81076 ( 933) SS BOND : bond 0.00589 ( 6) SS BOND : angle 0.88069 ( 12) covalent geometry : bond 0.00462 ( 6715) covalent geometry : angle 0.55556 ( 9124) *********************** 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 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.636 Fit side-chains REVERT: A 75 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6922 (tt0) REVERT: A 87 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6917 (pm20) REVERT: A 166 GLU cc_start: 0.6932 (tp30) cc_final: 0.6270 (tp30) REVERT: A 190 MET cc_start: 0.7515 (ttp) cc_final: 0.7209 (ttp) REVERT: A 231 GLU cc_start: 0.8100 (tp30) cc_final: 0.7473 (mm-30) REVERT: A 232 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7569 (mm-30) REVERT: A 259 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 470 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7221 (mptt) REVERT: A 480 MET cc_start: 0.8132 (mtm) cc_final: 0.7901 (mtm) REVERT: A 557 MET cc_start: 0.8796 (tmm) cc_final: 0.8545 (ttp) REVERT: A 577 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7446 (ttpp) REVERT: A 578 ASN cc_start: 0.7469 (p0) cc_final: 0.7032 (t0) REVERT: A 597 ASP cc_start: 0.8070 (t70) cc_final: 0.7559 (t0) REVERT: A 600 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7272 (pttm) REVERT: B 391 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6986 (m) REVERT: B 420 ASP cc_start: 0.8949 (m-30) cc_final: 0.8361 (m-30) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.1928 time to fit residues: 23.8850 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 391 CYS 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 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.132475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103194 restraints weight = 7112.989| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.06 r_work: 0.2949 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6734 Z= 0.177 Angle : 0.575 6.796 9175 Z= 0.280 Chirality : 0.042 0.163 985 Planarity : 0.004 0.029 1162 Dihedral : 4.605 33.964 1118 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.92 % Allowed : 11.95 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 776 helix: 1.55 (0.26), residues: 392 sheet: -0.29 (0.58), residues: 54 loop : -0.15 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.002 PHE A 369 TYR 0.019 0.002 TYR A 385 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 8) link_NAG-ASN : angle 3.21630 ( 24) link_BETA1-4 : bond 0.00452 ( 5) link_BETA1-4 : angle 1.86940 ( 15) hydrogen bonds : bond 0.05089 ( 334) hydrogen bonds : angle 4.81771 ( 933) SS BOND : bond 0.00567 ( 6) SS BOND : angle 0.79319 ( 12) covalent geometry : bond 0.00426 ( 6715) covalent geometry : angle 0.54690 ( 9124) *********************** 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 101 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.664 Fit side-chains REVERT: A 75 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6950 (tt0) REVERT: A 87 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6923 (pm20) REVERT: A 166 GLU cc_start: 0.6956 (tp30) cc_final: 0.6313 (tp30) REVERT: A 190 MET cc_start: 0.7504 (ttp) cc_final: 0.7210 (ttp) REVERT: A 231 GLU cc_start: 0.8086 (tp30) cc_final: 0.7465 (mm-30) REVERT: A 232 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7560 (mm-30) REVERT: A 259 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8155 (tt) REVERT: A 470 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7287 (mptt) REVERT: A 480 MET cc_start: 0.8104 (mtm) cc_final: 0.7873 (mtm) REVERT: A 557 MET cc_start: 0.8819 (tmm) cc_final: 0.8550 (ttp) REVERT: A 577 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7517 (ttpp) REVERT: A 578 ASN cc_start: 0.7479 (p0) cc_final: 0.7054 (t0) REVERT: A 597 ASP cc_start: 0.8071 (t70) cc_final: 0.7625 (t0) REVERT: A 600 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7312 (pttm) REVERT: B 391 CYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6957 (m) REVERT: B 420 ASP cc_start: 0.8933 (m-30) cc_final: 0.8341 (m-30) outliers start: 20 outliers final: 15 residues processed: 92 average time/residue: 0.1783 time to fit residues: 22.3756 Evaluate side-chains 98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 43 optimal weight: 0.0870 chunk 59 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 overall best weight: 0.1714 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.138666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110010 restraints weight = 7031.634| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.03 r_work: 0.2998 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6734 Z= 0.107 Angle : 0.507 6.697 9175 Z= 0.248 Chirality : 0.040 0.174 985 Planarity : 0.003 0.028 1162 Dihedral : 4.300 31.188 1118 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.04 % Allowed : 12.24 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.29), residues: 776 helix: 1.89 (0.26), residues: 377 sheet: 0.20 (0.65), residues: 44 loop : -0.10 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 PHE 0.012 0.001 PHE A 315 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 8) link_NAG-ASN : angle 2.99580 ( 24) link_BETA1-4 : bond 0.00499 ( 5) link_BETA1-4 : angle 1.77339 ( 15) hydrogen bonds : bond 0.04389 ( 334) hydrogen bonds : angle 4.71244 ( 933) SS BOND : bond 0.00441 ( 6) SS BOND : angle 0.56363 ( 12) covalent geometry : bond 0.00229 ( 6715) covalent geometry : angle 0.47887 ( 9124) ********************** 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 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.680 Fit side-chains REVERT: A 75 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6938 (tt0) REVERT: A 87 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6989 (pm20) REVERT: A 102 GLN cc_start: 0.7370 (pt0) cc_final: 0.6921 (mt0) REVERT: A 123 MET cc_start: 0.6443 (mtt) cc_final: 0.6230 (mtt) REVERT: A 190 MET cc_start: 0.7375 (ttp) cc_final: 0.7125 (ttp) REVERT: A 231 GLU cc_start: 0.8071 (tp30) cc_final: 0.7477 (mm-30) REVERT: A 232 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7523 (mm-30) REVERT: A 249 MET cc_start: 0.7348 (mtp) cc_final: 0.7143 (mtp) REVERT: A 259 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 470 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7292 (mptt) REVERT: A 577 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7532 (ttpp) REVERT: A 578 ASN cc_start: 0.7335 (p0) cc_final: 0.6941 (t0) REVERT: A 597 ASP cc_start: 0.8059 (t70) cc_final: 0.7575 (t0) REVERT: A 600 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7243 (pttm) REVERT: B 391 CYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6931 (m) REVERT: B 420 ASP cc_start: 0.8870 (m-30) cc_final: 0.8336 (m-30) outliers start: 14 outliers final: 11 residues processed: 86 average time/residue: 0.1812 time to fit residues: 21.4394 Evaluate side-chains 88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 427 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.2980 chunk 71 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.0060 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 57 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 overall best weight: 0.2396 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.136479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107208 restraints weight = 7139.218| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.09 r_work: 0.2989 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3266 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= 0.114 Angle : 0.510 6.306 9175 Z= 0.248 Chirality : 0.040 0.172 985 Planarity : 0.003 0.029 1162 Dihedral : 4.242 31.098 1118 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.90 % Allowed : 12.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 776 helix: 1.94 (0.26), residues: 377 sheet: 0.25 (0.65), residues: 44 loop : -0.06 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.005 0.001 HIS A 535 PHE 0.015 0.001 PHE A 369 TYR 0.017 0.001 TYR A 385 ARG 0.004 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 8) link_NAG-ASN : angle 2.94972 ( 24) link_BETA1-4 : bond 0.00461 ( 5) link_BETA1-4 : angle 1.70895 ( 15) hydrogen bonds : bond 0.04473 ( 334) hydrogen bonds : angle 4.67393 ( 933) SS BOND : bond 0.00455 ( 6) SS BOND : angle 0.64492 ( 12) covalent geometry : bond 0.00251 ( 6715) covalent geometry : angle 0.48335 ( 9124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5652.95 seconds wall clock time: 101 minutes 38.33 seconds (6098.33 seconds total)