Starting phenix.real_space_refine on Thu Jun 5 18:00:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whz_37553/06_2025/8whz_37553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whz_37553/06_2025/8whz_37553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8whz_37553/06_2025/8whz_37553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whz_37553/06_2025/8whz_37553.map" model { file = "/net/cci-nas-00/data/ceres_data/8whz_37553/06_2025/8whz_37553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whz_37553/06_2025/8whz_37553.cif" } resolution = 3.93 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= 0.044 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4173 2.51 5 N 1073 2.21 5 O 1230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 7.00, per 1000 atoms: 1.07 Number of scatterers: 6515 At special positions: 0 Unit cell: (75.97, 95.23, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1230 8.00 N 1073 7.00 C 4173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 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 391 " - pdb=" SG CYS B 525 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG B 601 " - " ASN B 354 " " NAG B 602 " - " ASN B 343 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 57.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.795A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.802A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) 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 194 removed outlier: 4.312A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) 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: 3.752A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.918A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.743A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.685A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.642A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.240A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) 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 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.753A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.827A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.532A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.894A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.806A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.788A 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 352 removed outlier: 3.666A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.875A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.523A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 903 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: 1.71 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1864 1.33 - 1.46: 1357 1.46 - 1.58: 3422 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6702 Sorted by residual: bond pdb=" C THR A 27 " pdb=" N PHE A 28 " ideal model delta sigma weight residual 1.335 1.292 0.043 1.30e-02 5.92e+03 1.12e+01 bond pdb=" N THR A 27 " pdb=" CA THR A 27 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.17e-02 7.31e+03 1.08e+01 bond pdb=" CA ARG B 457 " pdb=" CB ARG B 457 " ideal model delta sigma weight residual 1.534 1.480 0.053 1.78e-02 3.16e+03 8.94e+00 bond pdb=" CA THR A 27 " pdb=" C THR A 27 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.24e-02 6.50e+03 6.85e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.30e+00 ... (remaining 6697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8753 1.88 - 3.77: 312 3.77 - 5.65: 37 5.65 - 7.54: 6 7.54 - 9.42: 2 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N LYS A 313 " pdb=" CA LYS A 313 " pdb=" C LYS A 313 " ideal model delta sigma weight residual 111.82 106.74 5.08 1.16e+00 7.43e-01 1.92e+01 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 106.33 5.67 1.40e+00 5.10e-01 1.64e+01 angle pdb=" N CYS A 498 " pdb=" CA CYS A 498 " pdb=" C CYS A 498 " ideal model delta sigma weight residual 110.44 105.84 4.60 1.20e+00 6.94e-01 1.47e+01 angle pdb=" CA ARG B 457 " pdb=" C ARG B 457 " pdb=" N LYS B 458 " ideal model delta sigma weight residual 115.61 120.89 -5.28 1.45e+00 4.76e-01 1.32e+01 angle pdb=" N VAL A 364 " pdb=" CA VAL A 364 " pdb=" C VAL A 364 " ideal model delta sigma weight residual 106.21 109.67 -3.46 1.07e+00 8.73e-01 1.05e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3628 17.95 - 35.90: 318 35.90 - 53.85: 58 53.85 - 71.80: 17 71.80 - 89.75: 8 Dihedral angle restraints: 4029 sinusoidal: 1705 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 143.36 36.64 0 5.00e+00 4.00e-02 5.37e+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 93.00 134.85 -41.85 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.35 -36.35 1 1.00e+01 1.00e-02 1.87e+01 ... (remaining 4026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 705 0.049 - 0.097: 202 0.097 - 0.146: 54 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" C PRO B 384 " pdb=" CB PRO B 384 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CG LEU B 492 " pdb=" CB LEU B 492 " pdb=" CD1 LEU B 492 " pdb=" CD2 LEU B 492 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.072 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B 384 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 69 " -0.016 2.00e-02 2.50e+03 1.13e-02 3.22e+00 pdb=" CG TRP A 69 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 69 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 69 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 69 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 506 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 507 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.021 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 45 2.48 - 3.08: 4740 3.08 - 3.69: 10301 3.69 - 4.29: 14541 4.29 - 4.90: 22781 Nonbonded interactions: 52408 Sorted by model distance: nonbonded pdb=" O TYR B 421 " pdb=" CZ ARG B 457 " model vdw 1.873 3.270 nonbonded pdb=" O TYR B 421 " pdb=" NH1 ARG B 457 " model vdw 1.994 3.120 nonbonded pdb=" NH2 ARG B 454 " pdb=" CG ARG B 457 " model vdw 2.068 3.520 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.142 3.040 nonbonded pdb=" CZ ARG B 454 " pdb=" NE ARG B 457 " model vdw 2.171 3.350 ... (remaining 52403 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 670.540 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 24.350 Find NCS groups from input model: 0.060 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:3.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 699.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 6717 Z= 0.208 Angle : 0.801 9.421 9142 Z= 0.458 Chirality : 0.047 0.243 964 Planarity : 0.006 0.105 1172 Dihedral : 14.476 89.752 2516 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.54 (0.30), residues: 787 helix: 0.61 (0.26), residues: 390 sheet: -0.55 (0.89), residues: 35 loop : -1.43 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 69 HIS 0.004 0.001 HIS A 493 PHE 0.014 0.002 PHE A 230 TYR 0.020 0.002 TYR A 454 ARG 0.006 0.001 ARG A 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 6) link_NAG-ASN : angle 2.70915 ( 18) hydrogen bonds : bond 0.15190 ( 315) hydrogen bonds : angle 6.20077 ( 903) metal coordination : bond 0.00062 ( 2) SS BOND : bond 0.00183 ( 7) SS BOND : angle 1.52970 ( 14) covalent geometry : bond 0.00414 ( 6702) covalent geometry : angle 0.79127 ( 9110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6456 (mtp) cc_final: 0.6177 (mmm) REVERT: A 243 TYR cc_start: 0.9040 (t80) cc_final: 0.8669 (t80) REVERT: A 270 MET cc_start: 0.7170 (tpt) cc_final: 0.6916 (tpt) REVERT: A 333 LEU cc_start: 0.9346 (mt) cc_final: 0.9130 (mm) REVERT: A 408 MET cc_start: 0.8318 (mmp) cc_final: 0.8081 (mmt) REVERT: A 461 TRP cc_start: 0.8963 (m-10) cc_final: 0.8732 (m-10) REVERT: A 484 ILE cc_start: 0.8728 (mm) cc_final: 0.8257 (tp) REVERT: B 406 GLU cc_start: 0.8224 (mp0) cc_final: 0.8015 (mp0) outliers start: 2 outliers final: 1 residues processed: 202 average time/residue: 0.2543 time to fit residues: 66.2735 Evaluate side-chains 124 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 58 ASN A 60 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN B 417 ASN B 505 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.114739 restraints weight = 16059.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118189 restraints weight = 8969.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.120575 restraints weight = 6099.833| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6717 Z= 0.182 Angle : 0.713 8.078 9142 Z= 0.368 Chirality : 0.047 0.219 964 Planarity : 0.006 0.054 1172 Dihedral : 6.087 51.790 985 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.73 % Allowed : 10.79 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.40 (0.29), residues: 787 helix: 0.59 (0.25), residues: 406 sheet: -0.42 (0.80), residues: 42 loop : -1.28 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 165 HIS 0.005 0.001 HIS A 417 PHE 0.034 0.003 PHE B 375 TYR 0.022 0.002 TYR B 421 ARG 0.009 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 6) link_NAG-ASN : angle 3.05772 ( 18) hydrogen bonds : bond 0.05108 ( 315) hydrogen bonds : angle 5.00033 ( 903) metal coordination : bond 0.00150 ( 2) SS BOND : bond 0.00275 ( 7) SS BOND : angle 1.63187 ( 14) covalent geometry : bond 0.00408 ( 6702) covalent geometry : angle 0.69820 ( 9110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 TYR cc_start: 0.8918 (t80) cc_final: 0.8690 (t80) REVERT: A 323 MET cc_start: 0.8299 (mmt) cc_final: 0.7259 (mmm) REVERT: A 360 MET cc_start: 0.8382 (ppp) cc_final: 0.8032 (ppp) REVERT: A 366 MET cc_start: 0.8707 (ppp) cc_final: 0.7920 (ppp) REVERT: A 467 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 468 ILE cc_start: 0.8683 (mm) cc_final: 0.7948 (mm) REVERT: A 473 TRP cc_start: 0.7428 (m-10) cc_final: 0.7148 (m-10) REVERT: A 480 MET cc_start: 0.8740 (mtm) cc_final: 0.8532 (mtp) REVERT: A 557 MET cc_start: 0.8460 (tmm) cc_final: 0.8160 (ttp) REVERT: B 347 PHE cc_start: 0.6219 (m-80) cc_final: 0.5790 (m-80) REVERT: B 349 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8141 (p) outliers start: 19 outliers final: 8 residues processed: 142 average time/residue: 0.1918 time to fit residues: 36.4990 Evaluate side-chains 115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 64 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS B 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.143494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114908 restraints weight = 16053.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118486 restraints weight = 8965.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.120920 restraints weight = 6058.607| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6717 Z= 0.135 Angle : 0.641 9.303 9142 Z= 0.330 Chirality : 0.044 0.215 964 Planarity : 0.005 0.048 1172 Dihedral : 5.567 46.790 984 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.58 % Allowed : 15.54 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.23 (0.29), residues: 787 helix: 0.68 (0.25), residues: 406 sheet: 0.18 (0.83), residues: 42 loop : -1.20 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.017 0.001 PHE A 369 TYR 0.014 0.001 TYR A 237 ARG 0.004 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 6) link_NAG-ASN : angle 2.46968 ( 18) hydrogen bonds : bond 0.04674 ( 315) hydrogen bonds : angle 4.80509 ( 903) metal coordination : bond 0.00102 ( 2) SS BOND : bond 0.00189 ( 7) SS BOND : angle 1.41614 ( 14) covalent geometry : bond 0.00298 ( 6702) covalent geometry : angle 0.63041 ( 9110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7938 (mm) cc_final: 0.7039 (mm) REVERT: A 243 TYR cc_start: 0.8868 (t80) cc_final: 0.8637 (t80) REVERT: A 323 MET cc_start: 0.8417 (mmt) cc_final: 0.7062 (mmm) REVERT: A 366 MET cc_start: 0.8577 (ppp) cc_final: 0.7908 (ppp) REVERT: A 376 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7795 (tpt) REVERT: A 423 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 441 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8399 (ttpp) REVERT: A 467 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7068 (tm-30) REVERT: A 468 ILE cc_start: 0.8557 (mm) cc_final: 0.7640 (mm) REVERT: B 340 GLU cc_start: 0.6917 (mp0) cc_final: 0.6535 (mp0) REVERT: B 347 PHE cc_start: 0.6456 (m-80) cc_final: 0.6144 (m-80) outliers start: 11 outliers final: 4 residues processed: 127 average time/residue: 0.1850 time to fit residues: 31.2871 Evaluate side-chains 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 64 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS A 598 GLN B 439 ASN B 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.140515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.112410 restraints weight = 16268.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115793 restraints weight = 8902.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118043 restraints weight = 5988.859| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.843 6717 Z= 0.373 Angle : 0.628 6.685 9142 Z= 0.328 Chirality : 0.044 0.204 964 Planarity : 0.005 0.046 1172 Dihedral : 5.419 36.838 984 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 2.73 % Allowed : 16.83 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.10 (0.29), residues: 787 helix: 0.75 (0.25), residues: 400 sheet: 0.57 (0.81), residues: 42 loop : -1.10 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 594 HIS 0.004 0.001 HIS A 374 PHE 0.034 0.002 PHE B 375 TYR 0.015 0.002 TYR A 237 ARG 0.004 0.001 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 2.13900 ( 18) hydrogen bonds : bond 0.04697 ( 315) hydrogen bonds : angle 4.76196 ( 903) metal coordination : bond 0.59636 ( 2) SS BOND : bond 0.00234 ( 7) SS BOND : angle 1.20803 ( 14) covalent geometry : bond 0.00323 ( 6702) covalent geometry : angle 0.61984 ( 9110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8359 (t-100) cc_final: 0.7674 (t60) REVERT: A 249 MET cc_start: 0.8345 (mtp) cc_final: 0.7482 (mpp) REVERT: A 366 MET cc_start: 0.8612 (ppp) cc_final: 0.7903 (ppp) REVERT: A 406 GLU cc_start: 0.8526 (tp30) cc_final: 0.8314 (mm-30) REVERT: A 441 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8423 (ttpp) REVERT: A 468 ILE cc_start: 0.8606 (mm) cc_final: 0.8276 (mm) REVERT: B 347 PHE cc_start: 0.6245 (m-80) cc_final: 0.5856 (m-80) REVERT: B 349 SER cc_start: 0.8531 (m) cc_final: 0.8324 (p) REVERT: B 406 GLU cc_start: 0.7941 (mp0) cc_final: 0.7589 (mp0) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 0.1783 time to fit residues: 29.4436 Evaluate side-chains 110 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS A 380 GLN B 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.140615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112943 restraints weight = 16193.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116167 restraints weight = 9159.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.118371 restraints weight = 6267.143| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.845 6717 Z= 0.370 Angle : 0.612 8.095 9142 Z= 0.321 Chirality : 0.044 0.204 964 Planarity : 0.005 0.048 1172 Dihedral : 5.080 36.762 984 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 2.45 % Allowed : 18.42 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.04 (0.29), residues: 787 helix: 0.83 (0.25), residues: 408 sheet: 0.99 (0.95), residues: 30 loop : -1.14 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 594 HIS 0.006 0.001 HIS A 345 PHE 0.016 0.001 PHE B 490 TYR 0.022 0.002 TYR A 243 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 6) link_NAG-ASN : angle 1.96796 ( 18) hydrogen bonds : bond 0.04428 ( 315) hydrogen bonds : angle 4.65608 ( 903) metal coordination : bond 0.59788 ( 2) SS BOND : bond 0.00771 ( 7) SS BOND : angle 1.66665 ( 14) covalent geometry : bond 0.00286 ( 6702) covalent geometry : angle 0.60343 ( 9110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7044 (mmt) cc_final: 0.6427 (mmm) REVERT: A 163 TRP cc_start: 0.8411 (t-100) cc_final: 0.8147 (t60) REVERT: A 323 MET cc_start: 0.8381 (mmm) cc_final: 0.6959 (mmm) REVERT: A 366 MET cc_start: 0.8540 (ppp) cc_final: 0.7903 (ppp) REVERT: A 376 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7676 (tpt) REVERT: A 441 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8462 (ttpp) REVERT: A 480 MET cc_start: 0.8705 (mtt) cc_final: 0.8424 (mtm) REVERT: B 347 PHE cc_start: 0.6381 (m-80) cc_final: 0.5988 (m-80) REVERT: B 349 SER cc_start: 0.8667 (m) cc_final: 0.8271 (p) REVERT: B 406 GLU cc_start: 0.7828 (mp0) cc_final: 0.7546 (mp0) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.1749 time to fit residues: 28.7087 Evaluate side-chains 113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.139342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111793 restraints weight = 15954.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.114987 restraints weight = 9080.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.117122 restraints weight = 6241.190| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.852 6717 Z= 0.371 Angle : 0.609 6.655 9142 Z= 0.321 Chirality : 0.044 0.194 964 Planarity : 0.005 0.044 1172 Dihedral : 5.008 36.544 984 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.88 % Allowed : 20.43 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.05 (0.29), residues: 787 helix: 0.87 (0.25), residues: 404 sheet: 1.04 (0.76), residues: 40 loop : -1.09 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.033 0.001 PHE B 375 TYR 0.013 0.001 TYR A 237 ARG 0.007 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 6) link_NAG-ASN : angle 1.83398 ( 18) hydrogen bonds : bond 0.04471 ( 315) hydrogen bonds : angle 4.60271 ( 903) metal coordination : bond 0.60240 ( 2) SS BOND : bond 0.00543 ( 7) SS BOND : angle 2.25668 ( 14) covalent geometry : bond 0.00295 ( 6702) covalent geometry : angle 0.59782 ( 9110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8968 (m110) cc_final: 0.8575 (m-40) REVERT: A 152 MET cc_start: 0.7111 (mmt) cc_final: 0.6741 (mmm) REVERT: A 163 TRP cc_start: 0.8474 (t-100) cc_final: 0.8244 (t60) REVERT: A 249 MET cc_start: 0.8195 (mtp) cc_final: 0.7171 (mpp) REVERT: A 323 MET cc_start: 0.8341 (mmm) cc_final: 0.6946 (mmm) REVERT: A 366 MET cc_start: 0.8546 (ppp) cc_final: 0.7917 (ppp) REVERT: A 376 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7760 (tpt) REVERT: A 406 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8574 (mm-30) REVERT: A 441 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8479 (ttpp) REVERT: A 461 TRP cc_start: 0.8961 (m-10) cc_final: 0.8678 (m-10) REVERT: B 347 PHE cc_start: 0.6134 (m-80) cc_final: 0.5828 (m-80) REVERT: B 349 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8217 (p) outliers start: 20 outliers final: 10 residues processed: 121 average time/residue: 0.1613 time to fit residues: 27.0040 Evaluate side-chains 108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 49 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.0010 overall best weight: 0.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.140251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.113126 restraints weight = 16168.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116320 restraints weight = 9147.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118484 restraints weight = 6256.730| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6717 Z= 0.123 Angle : 0.606 9.689 9142 Z= 0.318 Chirality : 0.043 0.195 964 Planarity : 0.004 0.050 1172 Dihedral : 4.758 34.716 984 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 3.02 % Allowed : 21.44 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.02 (0.29), residues: 787 helix: 0.86 (0.25), residues: 408 sheet: 1.07 (0.76), residues: 41 loop : -1.17 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE B 490 TYR 0.013 0.001 TYR A 237 ARG 0.007 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 6) link_NAG-ASN : angle 1.64994 ( 18) hydrogen bonds : bond 0.04327 ( 315) hydrogen bonds : angle 4.53643 ( 903) metal coordination : bond 0.01455 ( 2) SS BOND : bond 0.00403 ( 7) SS BOND : angle 1.77080 ( 14) covalent geometry : bond 0.00263 ( 6702) covalent geometry : angle 0.59844 ( 9110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8976 (m110) cc_final: 0.8565 (m-40) REVERT: A 152 MET cc_start: 0.6892 (mmt) cc_final: 0.6545 (mmm) REVERT: A 163 TRP cc_start: 0.8508 (t-100) cc_final: 0.8259 (t60) REVERT: A 306 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8182 (ttp-170) REVERT: A 323 MET cc_start: 0.8310 (mmm) cc_final: 0.6827 (mmm) REVERT: A 366 MET cc_start: 0.8454 (ppp) cc_final: 0.7823 (ppp) REVERT: A 376 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7720 (tpt) REVERT: A 406 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8577 (mm-30) REVERT: A 441 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8497 (ttpp) REVERT: A 461 TRP cc_start: 0.8908 (m-10) cc_final: 0.8512 (m-10) REVERT: A 471 ASP cc_start: 0.8893 (p0) cc_final: 0.8679 (p0) REVERT: A 512 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8364 (t80) REVERT: A 560 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8751 (mt) outliers start: 21 outliers final: 11 residues processed: 115 average time/residue: 0.1578 time to fit residues: 25.5498 Evaluate side-chains 110 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 560 LEU 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 407 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.137002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.109581 restraints weight = 16089.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.112723 restraints weight = 9034.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.114850 restraints weight = 6163.662| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.6567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6717 Z= 0.139 Angle : 0.613 9.029 9142 Z= 0.321 Chirality : 0.044 0.183 964 Planarity : 0.005 0.050 1172 Dihedral : 4.862 34.170 984 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 2.30 % Allowed : 22.88 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.17 (0.29), residues: 787 helix: 1.10 (0.26), residues: 393 sheet: 1.00 (0.80), residues: 41 loop : -1.15 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 473 HIS 0.006 0.001 HIS A 345 PHE 0.030 0.002 PHE B 375 TYR 0.015 0.002 TYR A 237 ARG 0.007 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 6) link_NAG-ASN : angle 1.69310 ( 18) hydrogen bonds : bond 0.04467 ( 315) hydrogen bonds : angle 4.54386 ( 903) metal coordination : bond 0.00110 ( 2) SS BOND : bond 0.00374 ( 7) SS BOND : angle 1.42797 ( 14) covalent geometry : bond 0.00312 ( 6702) covalent geometry : angle 0.60648 ( 9110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8999 (m110) cc_final: 0.8566 (m-40) REVERT: A 152 MET cc_start: 0.7139 (mmt) cc_final: 0.6770 (mmm) REVERT: A 163 TRP cc_start: 0.8480 (t-100) cc_final: 0.8275 (t60) REVERT: A 234 LYS cc_start: 0.9386 (ptmm) cc_final: 0.9133 (pttp) REVERT: A 280 SER cc_start: 0.8843 (m) cc_final: 0.8610 (p) REVERT: A 306 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.8192 (ttp-170) REVERT: A 323 MET cc_start: 0.8323 (mmm) cc_final: 0.6960 (mmm) REVERT: A 366 MET cc_start: 0.8364 (ppp) cc_final: 0.7815 (ppp) REVERT: A 376 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7779 (tpt) REVERT: A 406 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8633 (mm-30) REVERT: A 441 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8659 (ttpp) REVERT: A 461 TRP cc_start: 0.8948 (m-10) cc_final: 0.8655 (m-10) REVERT: A 560 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8772 (mt) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.1537 time to fit residues: 24.3491 Evaluate side-chains 111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 349 SER 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 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108054 restraints weight = 16141.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.111138 restraints weight = 9034.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.113203 restraints weight = 6176.325| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6717 Z= 0.151 Angle : 0.640 8.414 9142 Z= 0.334 Chirality : 0.044 0.181 964 Planarity : 0.005 0.050 1172 Dihedral : 5.050 35.212 984 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 2.45 % Allowed : 23.74 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.17 (0.30), residues: 787 helix: 1.10 (0.26), residues: 393 sheet: 1.04 (0.77), residues: 41 loop : -1.15 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 473 HIS 0.008 0.001 HIS A 345 PHE 0.027 0.002 PHE A 464 TYR 0.014 0.002 TYR B 351 ARG 0.009 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 6) link_NAG-ASN : angle 1.68364 ( 18) hydrogen bonds : bond 0.04617 ( 315) hydrogen bonds : angle 4.57859 ( 903) metal coordination : bond 0.00074 ( 2) SS BOND : bond 0.00617 ( 7) SS BOND : angle 1.53635 ( 14) covalent geometry : bond 0.00341 ( 6702) covalent geometry : angle 0.63364 ( 9110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7900 (ppp) cc_final: 0.7391 (ppp) REVERT: A 121 ASN cc_start: 0.8991 (m110) cc_final: 0.8655 (m-40) REVERT: A 152 MET cc_start: 0.7293 (mmt) cc_final: 0.6897 (mmm) REVERT: A 163 TRP cc_start: 0.8562 (t-100) cc_final: 0.8300 (t60) REVERT: A 234 LYS cc_start: 0.9419 (ptmm) cc_final: 0.9152 (pttp) REVERT: A 249 MET cc_start: 0.8117 (mtt) cc_final: 0.7852 (mmm) REVERT: A 280 SER cc_start: 0.8836 (m) cc_final: 0.8610 (p) REVERT: A 306 ARG cc_start: 0.8427 (ttp-170) cc_final: 0.8173 (ttp-170) REVERT: A 323 MET cc_start: 0.8440 (mmm) cc_final: 0.7138 (mmm) REVERT: A 366 MET cc_start: 0.8460 (ppp) cc_final: 0.7811 (ppp) REVERT: A 376 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7769 (tpt) REVERT: A 406 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8661 (mm-30) REVERT: A 441 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8677 (ttpp) REVERT: A 461 TRP cc_start: 0.8974 (m-10) cc_final: 0.8686 (m-10) REVERT: A 512 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8318 (t80) REVERT: A 560 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8793 (mt) REVERT: B 454 ARG cc_start: 0.6768 (mtm110) cc_final: 0.6512 (mtm110) outliers start: 17 outliers final: 11 residues processed: 109 average time/residue: 0.2039 time to fit residues: 31.4430 Evaluate side-chains 109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 74 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.139027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.111520 restraints weight = 16210.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.114718 restraints weight = 9085.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116922 restraints weight = 6212.582| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6717 Z= 0.120 Angle : 0.628 9.928 9142 Z= 0.324 Chirality : 0.044 0.187 964 Planarity : 0.005 0.050 1172 Dihedral : 4.759 33.109 984 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.30 % Allowed : 23.88 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.29 (0.30), residues: 787 helix: 1.16 (0.26), residues: 397 sheet: 1.18 (0.79), residues: 41 loop : -1.07 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.030 0.001 PHE A 464 TYR 0.011 0.001 TYR A 237 ARG 0.007 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 6) link_NAG-ASN : angle 1.46831 ( 18) hydrogen bonds : bond 0.04216 ( 315) hydrogen bonds : angle 4.47211 ( 903) metal coordination : bond 0.00062 ( 2) SS BOND : bond 0.00404 ( 7) SS BOND : angle 1.45848 ( 14) covalent geometry : bond 0.00263 ( 6702) covalent geometry : angle 0.62347 ( 9110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7761 (ppp) cc_final: 0.7324 (ppp) REVERT: A 121 ASN cc_start: 0.9010 (m110) cc_final: 0.8674 (m-40) REVERT: A 152 MET cc_start: 0.7287 (mmt) cc_final: 0.6902 (mmm) REVERT: A 163 TRP cc_start: 0.8503 (t-100) cc_final: 0.8287 (t60) REVERT: A 234 LYS cc_start: 0.9391 (ptmm) cc_final: 0.9109 (pttp) REVERT: A 280 SER cc_start: 0.8803 (m) cc_final: 0.8590 (p) REVERT: A 287 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: A 306 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.8097 (ttp-170) REVERT: A 323 MET cc_start: 0.8315 (mmm) cc_final: 0.7082 (mmm) REVERT: A 366 MET cc_start: 0.8274 (ppp) cc_final: 0.7710 (ppp) REVERT: A 376 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7608 (tpt) REVERT: A 406 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8646 (mm-30) REVERT: A 441 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8742 (ttpp) REVERT: A 461 TRP cc_start: 0.8901 (m-10) cc_final: 0.8603 (m-10) REVERT: A 512 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8332 (t80) REVERT: A 560 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8778 (mt) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.1594 time to fit residues: 25.4577 Evaluate side-chains 112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 560 LEU 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 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.139041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.111493 restraints weight = 16364.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114734 restraints weight = 9166.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116911 restraints weight = 6245.151| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 6717 Z= 0.212 Angle : 1.091 59.148 9142 Z= 0.620 Chirality : 0.048 0.621 964 Planarity : 0.005 0.051 1172 Dihedral : 4.772 33.099 984 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.30 % Allowed : 24.60 % Favored : 73.09 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.50 % 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: 0.30 (0.30), residues: 787 helix: 1.16 (0.26), residues: 397 sheet: 1.20 (0.79), residues: 41 loop : -1.05 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.027 0.001 PHE A 464 TYR 0.011 0.001 TYR A 237 ARG 0.005 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 6) link_NAG-ASN : angle 1.48009 ( 18) hydrogen bonds : bond 0.04253 ( 315) hydrogen bonds : angle 4.53891 ( 903) metal coordination : bond 0.00055 ( 2) SS BOND : bond 0.00337 ( 7) SS BOND : angle 1.39425 ( 14) covalent geometry : bond 0.00494 ( 6702) covalent geometry : angle 1.08984 ( 9110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4010.18 seconds wall clock time: 71 minutes 28.73 seconds (4288.73 seconds total)