Starting phenix.real_space_refine on Thu Jun 5 20:41:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsa_32752/06_2025/7wsa_32752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsa_32752/06_2025/7wsa_32752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsa_32752/06_2025/7wsa_32752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsa_32752/06_2025/7wsa_32752.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsa_32752/06_2025/7wsa_32752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsa_32752/06_2025/7wsa_32752.cif" } resolution = 3.0 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= -0.004 sd= 0.028 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 37 5.16 5 C 4203 2.51 5 N 1084 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 6567 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.80, per 1000 atoms: 1.04 Number of scatterers: 6567 At special positions: 0 Unit cell: (74.048, 93.184, 121.472, 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 37 16.00 O 1243 8.00 N 1084 7.00 C 4203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 957.5 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 56.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.896A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.599A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.725A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.507A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.281A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.661A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.782A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.339A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.851A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.537A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.849A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.862A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.671A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.354A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.669A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.434A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.832A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.531A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.987A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.164A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 906 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: 1.74 Time building geometry restraints manager: 1.88 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: 1964 1.34 - 1.46: 1406 1.46 - 1.58: 3324 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6752 Sorted by residual: bond pdb=" CA ALA D 36 " pdb=" CB ALA D 36 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.57e-02 4.06e+03 8.94e+00 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.24e-02 6.50e+03 7.51e+00 bond pdb=" N GLN D 175 " pdb=" CA GLN D 175 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.32e-02 5.74e+03 6.84e+00 bond pdb=" N CYS D 261 " pdb=" CA CYS D 261 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.22e-02 6.72e+03 6.42e+00 bond pdb=" N ARG D 518 " pdb=" CA ARG D 518 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.22e+00 ... (remaining 6747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 8803 1.85 - 3.70: 315 3.70 - 5.55: 45 5.55 - 7.39: 12 7.39 - 9.24: 1 Bond angle restraints: 9176 Sorted by residual: angle pdb=" N GLU D 37 " pdb=" CA GLU D 37 " pdb=" C GLU D 37 " ideal model delta sigma weight residual 112.38 107.36 5.02 1.22e+00 6.72e-01 1.69e+01 angle pdb=" N LEU D 39 " pdb=" CA LEU D 39 " pdb=" C LEU D 39 " ideal model delta sigma weight residual 113.20 108.52 4.68 1.21e+00 6.83e-01 1.50e+01 angle pdb=" N GLN D 42 " pdb=" CA GLN D 42 " pdb=" C GLN D 42 " ideal model delta sigma weight residual 111.69 107.24 4.45 1.23e+00 6.61e-01 1.31e+01 angle pdb=" N LYS D 541 " pdb=" CA LYS D 541 " pdb=" C LYS D 541 " ideal model delta sigma weight residual 112.57 108.62 3.95 1.13e+00 7.83e-01 1.22e+01 angle pdb=" N PHE D 40 " pdb=" CA PHE D 40 " pdb=" C PHE D 40 " ideal model delta sigma weight residual 112.68 108.36 4.32 1.33e+00 5.65e-01 1.05e+01 ... (remaining 9171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3653 17.40 - 34.79: 352 34.79 - 52.19: 51 52.19 - 69.59: 18 69.59 - 86.98: 7 Dihedral angle restraints: 4081 sinusoidal: 1740 harmonic: 2341 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 28.66 64.34 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CA GLN D 139 " pdb=" C GLN D 139 " pdb=" N GLU D 140 " pdb=" CA GLU D 140 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 4078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 636 0.040 - 0.080: 228 0.080 - 0.120: 92 0.120 - 0.160: 20 0.160 - 0.200: 4 Chirality restraints: 980 Sorted by residual: chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA MET D 480 " pdb=" N MET D 480 " pdb=" C MET D 480 " pdb=" CB MET D 480 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 977 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 68 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C LYS D 68 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS D 68 " 0.025 2.00e-02 2.50e+03 pdb=" N TRP D 69 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 241 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C HIS D 241 " 0.051 2.00e-02 2.50e+03 pdb=" O HIS D 241 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA D 242 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 606 " -0.020 2.00e-02 2.50e+03 1.85e-02 8.53e+00 pdb=" CG TRP D 606 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 606 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 606 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 606 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 606 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 606 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 606 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 606 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 606 " 0.000 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 420 2.73 - 3.27: 6664 3.27 - 3.81: 10852 3.81 - 4.36: 13240 4.36 - 4.90: 22087 Nonbonded interactions: 53263 Sorted by model distance: nonbonded pdb=" OH TYR D 217 " pdb=" OD2 ASP D 225 " model vdw 2.185 3.040 nonbonded pdb=" NZ LYS D 475 " pdb=" OE1 GLU D 495 " model vdw 2.305 3.120 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASP D 367 " model vdw 2.334 3.040 nonbonded pdb=" NE ARG A 493 " pdb=" OE2 GLU D 35 " model vdw 2.339 3.120 ... (remaining 53258 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 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: 118.170 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.310 Find NCS groups from input model: 0.070 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 0.053 6765 Z= 0.214 Angle : 0.786 9.243 9209 Z= 0.440 Chirality : 0.049 0.200 980 Planarity : 0.008 0.072 1179 Dihedral : 13.937 86.985 2559 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.26), residues: 792 helix: -1.12 (0.22), residues: 388 sheet: 0.18 (0.63), residues: 54 loop : -1.01 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 606 HIS 0.006 0.001 HIS D 265 PHE 0.039 0.002 PHE D 274 TYR 0.020 0.001 TYR D 515 ARG 0.016 0.001 ARG D 582 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 1.62063 ( 21) hydrogen bonds : bond 0.16018 ( 314) hydrogen bonds : angle 6.81124 ( 906) SS BOND : bond 0.00536 ( 6) SS BOND : angle 1.67244 ( 12) covalent geometry : bond 0.00391 ( 6752) covalent geometry : angle 0.78143 ( 9176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.698 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.0756 time to fit residues: 123.0020 Evaluate side-chains 73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 71 optimal weight: 0.0370 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 98 GLN D 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.148365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.125927 restraints weight = 15417.695| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.77 r_work: 0.3960 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6765 Z= 0.119 Angle : 0.590 5.724 9209 Z= 0.302 Chirality : 0.043 0.177 980 Planarity : 0.005 0.045 1179 Dihedral : 5.592 55.047 1013 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.57 % Allowed : 10.11 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.28), residues: 792 helix: 0.16 (0.25), residues: 395 sheet: -0.24 (0.62), residues: 59 loop : -0.33 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 606 HIS 0.003 0.001 HIS D 241 PHE 0.022 0.001 PHE D 504 TYR 0.012 0.001 TYR D 385 ARG 0.005 0.001 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 7) link_NAG-ASN : angle 1.49895 ( 21) hydrogen bonds : bond 0.04456 ( 314) hydrogen bonds : angle 4.85272 ( 906) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.33195 ( 12) covalent geometry : bond 0.00253 ( 6752) covalent geometry : angle 0.58466 ( 9176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 LEU cc_start: 0.7615 (mp) cc_final: 0.7375 (mp) outliers start: 11 outliers final: 2 residues processed: 93 average time/residue: 0.9752 time to fit residues: 96.9043 Evaluate side-chains 75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 73 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 154 ASN D 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.149351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.127589 restraints weight = 15816.540| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.59 r_work: 0.3917 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6765 Z= 0.134 Angle : 0.609 9.184 9209 Z= 0.302 Chirality : 0.043 0.166 980 Planarity : 0.004 0.040 1179 Dihedral : 5.519 55.344 1013 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 13.82 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 792 helix: 0.59 (0.25), residues: 402 sheet: -0.16 (0.63), residues: 59 loop : -0.05 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 275 HIS 0.003 0.001 HIS D 374 PHE 0.014 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.004 0.001 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 7) link_NAG-ASN : angle 1.14904 ( 21) hydrogen bonds : bond 0.04406 ( 314) hydrogen bonds : angle 4.63877 ( 906) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.19200 ( 12) covalent geometry : bond 0.00291 ( 6752) covalent geometry : angle 0.60656 ( 9176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 290 ASN cc_start: 0.7671 (t0) cc_final: 0.7336 (t0) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.9354 time to fit residues: 87.2250 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 591 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.141362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.119612 restraints weight = 15406.338| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.67 r_work: 0.3873 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6765 Z= 0.168 Angle : 0.662 9.111 9209 Z= 0.332 Chirality : 0.046 0.203 980 Planarity : 0.004 0.043 1179 Dihedral : 6.044 58.815 1013 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.28 % Allowed : 13.82 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.29), residues: 792 helix: 0.68 (0.25), residues: 404 sheet: -0.06 (0.64), residues: 59 loop : -0.04 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 275 HIS 0.004 0.001 HIS D 374 PHE 0.022 0.001 PHE D 504 TYR 0.013 0.002 TYR D 158 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 7) link_NAG-ASN : angle 1.35463 ( 21) hydrogen bonds : bond 0.04906 ( 314) hydrogen bonds : angle 4.74203 ( 906) SS BOND : bond 0.00303 ( 6) SS BOND : angle 2.67344 ( 12) covalent geometry : bond 0.00374 ( 6752) covalent geometry : angle 0.65310 ( 9176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7618 (tm-30) REVERT: D 97 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8418 (mm) REVERT: D 290 ASN cc_start: 0.7761 (t0) cc_final: 0.7408 (t0) REVERT: D 594 TRP cc_start: 0.7577 (t-100) cc_final: 0.7335 (t-100) outliers start: 23 outliers final: 9 residues processed: 87 average time/residue: 0.8125 time to fit residues: 76.4317 Evaluate side-chains 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.140742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.119338 restraints weight = 15334.781| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.66 r_work: 0.3870 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6765 Z= 0.153 Angle : 0.650 8.972 9209 Z= 0.323 Chirality : 0.046 0.250 980 Planarity : 0.004 0.042 1179 Dihedral : 5.415 56.435 1013 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.71 % Allowed : 16.10 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.29), residues: 792 helix: 0.80 (0.26), residues: 401 sheet: 0.02 (0.63), residues: 59 loop : 0.09 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 275 HIS 0.004 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.017 0.001 TYR D 279 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 1.39140 ( 21) hydrogen bonds : bond 0.04548 ( 314) hydrogen bonds : angle 4.68718 ( 906) SS BOND : bond 0.00505 ( 6) SS BOND : angle 2.33472 ( 12) covalent geometry : bond 0.00343 ( 6752) covalent geometry : angle 0.64267 ( 9176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7663 (tm-30) REVERT: D 97 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8406 (mm) REVERT: D 194 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7189 (m110) REVERT: D 594 TRP cc_start: 0.7729 (t-100) cc_final: 0.7199 (t-100) outliers start: 19 outliers final: 7 residues processed: 81 average time/residue: 0.9424 time to fit residues: 81.7355 Evaluate side-chains 74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.141710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.120332 restraints weight = 15214.503| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.65 r_work: 0.3886 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6765 Z= 0.128 Angle : 0.641 9.511 9209 Z= 0.315 Chirality : 0.044 0.246 980 Planarity : 0.004 0.044 1179 Dihedral : 4.997 54.360 1013 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.71 % Allowed : 16.38 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.29), residues: 792 helix: 0.97 (0.26), residues: 395 sheet: -0.10 (0.62), residues: 59 loop : 0.07 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 PHE 0.020 0.001 PHE D 504 TYR 0.025 0.001 TYR A 380 ARG 0.009 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 1.21360 ( 21) hydrogen bonds : bond 0.04239 ( 314) hydrogen bonds : angle 4.61662 ( 906) SS BOND : bond 0.00547 ( 6) SS BOND : angle 2.22128 ( 12) covalent geometry : bond 0.00285 ( 6752) covalent geometry : angle 0.63401 ( 9176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 97 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8373 (mm) REVERT: D 161 ARG cc_start: 0.1769 (ttp-170) cc_final: 0.1198 (ttp-170) REVERT: D 194 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7223 (m110) outliers start: 19 outliers final: 6 residues processed: 84 average time/residue: 0.9098 time to fit residues: 82.0806 Evaluate side-chains 71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.141160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.119746 restraints weight = 15117.763| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.66 r_work: 0.3874 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6765 Z= 0.144 Angle : 0.677 11.424 9209 Z= 0.332 Chirality : 0.045 0.249 980 Planarity : 0.004 0.041 1179 Dihedral : 5.117 55.428 1013 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.99 % Allowed : 17.81 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.29), residues: 792 helix: 0.96 (0.26), residues: 401 sheet: 0.27 (0.64), residues: 54 loop : 0.12 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.037 0.001 TYR A 380 ARG 0.008 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 7) link_NAG-ASN : angle 1.26122 ( 21) hydrogen bonds : bond 0.04417 ( 314) hydrogen bonds : angle 4.62830 ( 906) SS BOND : bond 0.00605 ( 6) SS BOND : angle 2.42796 ( 12) covalent geometry : bond 0.00326 ( 6752) covalent geometry : angle 0.66996 ( 9176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 97 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8398 (mm) REVERT: D 194 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7227 (m110) outliers start: 21 outliers final: 10 residues processed: 82 average time/residue: 0.8622 time to fit residues: 76.0628 Evaluate side-chains 76 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.140340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.118766 restraints weight = 15238.394| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.68 r_work: 0.3858 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6765 Z= 0.154 Angle : 0.689 13.299 9209 Z= 0.337 Chirality : 0.046 0.251 980 Planarity : 0.004 0.041 1179 Dihedral : 5.223 55.689 1013 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.85 % Allowed : 18.66 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.29), residues: 792 helix: 0.94 (0.26), residues: 395 sheet: -0.08 (0.63), residues: 59 loop : 0.06 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 PHE 0.022 0.001 PHE D 504 TYR 0.027 0.001 TYR A 380 ARG 0.007 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 7) link_NAG-ASN : angle 1.37613 ( 21) hydrogen bonds : bond 0.04526 ( 314) hydrogen bonds : angle 4.69100 ( 906) SS BOND : bond 0.00690 ( 6) SS BOND : angle 2.25704 ( 12) covalent geometry : bond 0.00348 ( 6752) covalent geometry : angle 0.68247 ( 9176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 161 ARG cc_start: 0.1807 (ttp-170) cc_final: 0.1198 (ttt180) REVERT: D 194 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7243 (m110) outliers start: 20 outliers final: 8 residues processed: 83 average time/residue: 0.9722 time to fit residues: 86.2433 Evaluate side-chains 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 0.0060 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4134 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.141586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.120171 restraints weight = 15373.910| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.68 r_work: 0.3881 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6765 Z= 0.130 Angle : 0.684 12.285 9209 Z= 0.332 Chirality : 0.045 0.214 980 Planarity : 0.004 0.047 1179 Dihedral : 4.940 54.018 1013 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.14 % Allowed : 19.80 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.29), residues: 792 helix: 1.10 (0.26), residues: 388 sheet: 0.26 (0.64), residues: 54 loop : -0.01 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 275 HIS 0.003 0.001 HIS D 374 PHE 0.024 0.001 PHE D 452 TYR 0.013 0.001 TYR A 380 ARG 0.009 0.001 ARG D 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 7) link_NAG-ASN : angle 1.15181 ( 21) hydrogen bonds : bond 0.04115 ( 314) hydrogen bonds : angle 4.59820 ( 906) SS BOND : bond 0.00649 ( 6) SS BOND : angle 2.10555 ( 12) covalent geometry : bond 0.00294 ( 6752) covalent geometry : angle 0.67911 ( 9176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 364 ASP cc_start: 0.7119 (t0) cc_final: 0.6791 (t0) REVERT: D 152 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5690 (tpt) REVERT: D 161 ARG cc_start: 0.1721 (ttp-170) cc_final: 0.1127 (ttp-170) REVERT: D 194 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7353 (m110) REVERT: D 290 ASN cc_start: 0.7876 (t0) cc_final: 0.7609 (t0) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 1.0140 time to fit residues: 92.3303 Evaluate side-chains 74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN D 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.139708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.118265 restraints weight = 15354.274| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.67 r_work: 0.3847 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6765 Z= 0.170 Angle : 0.741 12.296 9209 Z= 0.360 Chirality : 0.047 0.203 980 Planarity : 0.004 0.042 1179 Dihedral : 5.337 56.522 1013 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.85 % Allowed : 21.37 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.29), residues: 792 helix: 0.89 (0.26), residues: 397 sheet: -0.06 (0.64), residues: 59 loop : -0.07 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 275 HIS 0.004 0.001 HIS D 505 PHE 0.037 0.001 PHE D 452 TYR 0.020 0.001 TYR D 515 ARG 0.009 0.001 ARG D 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 7) link_NAG-ASN : angle 1.47662 ( 21) hydrogen bonds : bond 0.04724 ( 314) hydrogen bonds : angle 4.76804 ( 906) SS BOND : bond 0.00611 ( 6) SS BOND : angle 2.08078 ( 12) covalent geometry : bond 0.00386 ( 6752) covalent geometry : angle 0.73504 ( 9176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 364 ASP cc_start: 0.7184 (t0) cc_final: 0.6867 (t0) REVERT: D 115 ARG cc_start: 0.6221 (tpt-90) cc_final: 0.5717 (ptm-80) REVERT: D 161 ARG cc_start: 0.1931 (ttp-170) cc_final: 0.1181 (ttt180) REVERT: D 290 ASN cc_start: 0.7908 (t0) cc_final: 0.7661 (t0) REVERT: D 556 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7779 (p0) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.9148 time to fit residues: 80.5135 Evaluate side-chains 77 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 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 = 0.4231 r_free = 0.4231 target = 0.139565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.118317 restraints weight = 15397.760| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.64 r_work: 0.3851 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 6765 Z= 0.231 Angle : 1.099 59.199 9209 Z= 0.631 Chirality : 0.063 1.356 980 Planarity : 0.005 0.084 1179 Dihedral : 5.360 56.465 1013 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.57 % Allowed : 21.65 % Favored : 76.78 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.29), residues: 792 helix: 0.89 (0.26), residues: 397 sheet: -0.07 (0.64), residues: 59 loop : -0.07 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 275 HIS 0.003 0.001 HIS D 505 PHE 0.030 0.001 PHE D 452 TYR 0.012 0.001 TYR D 515 ARG 0.013 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 7) link_NAG-ASN : angle 1.47661 ( 21) hydrogen bonds : bond 0.04729 ( 314) hydrogen bonds : angle 4.77926 ( 906) SS BOND : bond 0.00910 ( 6) SS BOND : angle 4.09508 ( 12) covalent geometry : bond 0.00481 ( 6752) covalent geometry : angle 1.08912 ( 9176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4724.97 seconds wall clock time: 81 minutes 52.57 seconds (4912.57 seconds total)