Starting phenix.real_space_refine on Tue Feb 11 21:35:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsa_32752/02_2025/7wsa_32752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsa_32752/02_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_32752/02_2025/7wsa_32752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsa_32752/02_2025/7wsa_32752.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsa_32752/02_2025/7wsa_32752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsa_32752/02_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-5592/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: 6.30, per 1000 atoms: 0.96 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: 1.43 Conformation dependent library (CDL) restraints added in 882.9 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: 0.72 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: 1.75 Time building geometry restraints manager: 1.74 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: 13.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.260 Find NCS groups from input model: 0.070 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- 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 6752 Z= 0.256 Angle : 0.781 9.243 9176 Z= 0.439 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 *********************** 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 : 0.777 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.0970 time to fit residues: 125.5019 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 : 0.732 ------------------------------------------------------------------------------- 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: 0.2980 chunk 71 optimal weight: 0.0370 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.148592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.126238 restraints weight = 15392.408| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.76 r_work: 0.3966 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6752 Z= 0.156 Angle : 0.582 5.842 9176 Z= 0.298 Chirality : 0.043 0.176 980 Planarity : 0.005 0.043 1179 Dihedral : 5.506 55.037 1013 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.57 % Allowed : 10.54 % Favored : 87.89 % 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: -0.17 (0.28), residues: 792 helix: 0.19 (0.25), residues: 396 sheet: -0.24 (0.62), residues: 59 loop : -0.28 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 606 HIS 0.003 0.001 HIS D 241 PHE 0.023 0.001 PHE D 504 TYR 0.010 0.001 TYR D 158 ARG 0.005 0.001 ARG D 273 *********************** 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 : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 290 ASN cc_start: 0.7659 (t0) cc_final: 0.7234 (t0) outliers start: 11 outliers final: 2 residues processed: 93 average time/residue: 0.9769 time to fit residues: 96.8951 Evaluate side-chains 73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.147073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.125102 restraints weight = 15761.344| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.61 r_work: 0.3878 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6752 Z= 0.246 Angle : 0.656 9.666 9176 Z= 0.332 Chirality : 0.046 0.171 980 Planarity : 0.004 0.043 1179 Dihedral : 6.052 56.740 1013 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.56 % Allowed : 13.96 % Favored : 83.48 % 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: 0.16 (0.29), residues: 792 helix: 0.43 (0.25), residues: 405 sheet: -0.27 (0.61), residues: 60 loop : -0.03 (0.34), residues: 327 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 0.015 0.002 PHE D 369 TYR 0.016 0.002 TYR D 237 ARG 0.004 0.001 ARG D 273 *********************** 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 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 290 ASN cc_start: 0.7709 (t0) cc_final: 0.7434 (t0) outliers start: 18 outliers final: 8 residues processed: 80 average time/residue: 0.9448 time to fit residues: 81.4534 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 580 ASN 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: 0.8980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.118933 restraints weight = 15389.264| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.70 r_work: 0.3861 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6752 Z= 0.242 Angle : 0.656 8.775 9176 Z= 0.329 Chirality : 0.046 0.233 980 Planarity : 0.004 0.043 1179 Dihedral : 5.698 56.580 1013 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.85 % Allowed : 14.67 % Favored : 82.48 % 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: 0.57 (0.25), residues: 404 sheet: -0.06 (0.63), residues: 59 loop : -0.06 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 275 HIS 0.004 0.001 HIS D 265 PHE 0.019 0.001 PHE D 504 TYR 0.013 0.001 TYR D 158 ARG 0.004 0.001 ARG A 357 *********************** 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 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 97 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8387 (mm) REVERT: D 290 ASN cc_start: 0.7774 (t0) cc_final: 0.7429 (t0) outliers start: 20 outliers final: 8 residues processed: 81 average time/residue: 0.9564 time to fit residues: 83.0441 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 : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE 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 324 THR 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: 0.6980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.141362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.119917 restraints weight = 15348.964| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.64 r_work: 0.3877 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6752 Z= 0.196 Angle : 0.635 8.320 9176 Z= 0.316 Chirality : 0.044 0.225 980 Planarity : 0.004 0.042 1179 Dihedral : 5.199 54.958 1013 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.42 % Allowed : 16.10 % Favored : 81.48 % 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: 0.50 (0.29), residues: 792 helix: 0.75 (0.26), residues: 402 sheet: -0.05 (0.64), residues: 59 loop : 0.06 (0.34), residues: 331 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 0.012 0.001 PHE D 369 TYR 0.014 0.001 TYR D 279 ARG 0.006 0.000 ARG A 357 *********************** 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 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 97 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 290 ASN cc_start: 0.7683 (t0) cc_final: 0.7418 (t0) outliers start: 17 outliers final: 9 residues processed: 85 average time/residue: 1.0187 time to fit residues: 92.3491 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 : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.140467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.119010 restraints weight = 15107.581| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.66 r_work: 0.3863 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6752 Z= 0.214 Angle : 0.679 17.020 9176 Z= 0.331 Chirality : 0.046 0.275 980 Planarity : 0.004 0.041 1179 Dihedral : 5.197 55.395 1013 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.99 % Allowed : 16.95 % Favored : 80.06 % 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: 0.59 (0.29), residues: 792 helix: 0.91 (0.26), residues: 395 sheet: 0.24 (0.66), residues: 54 loop : -0.07 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 275 HIS 0.003 0.001 HIS D 374 PHE 0.019 0.001 PHE D 504 TYR 0.018 0.001 TYR A 380 ARG 0.005 0.000 ARG A 357 *********************** 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 94 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 97 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8389 (mm) REVERT: D 161 ARG cc_start: 0.1679 (ttp-170) cc_final: 0.1069 (ttp-170) REVERT: D 290 ASN cc_start: 0.7685 (t0) cc_final: 0.7429 (t0) REVERT: D 598 GLN cc_start: 0.5939 (mt0) cc_final: 0.5622 (tp-100) outliers start: 21 outliers final: 9 residues processed: 85 average time/residue: 0.9701 time to fit residues: 88.3237 Evaluate side-chains 75 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.140178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.118677 restraints weight = 15051.775| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.63 r_work: 0.3856 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6752 Z= 0.220 Angle : 0.680 15.151 9176 Z= 0.333 Chirality : 0.045 0.239 980 Planarity : 0.004 0.045 1179 Dihedral : 5.292 56.325 1013 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.13 % Allowed : 17.95 % Favored : 78.92 % 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: 0.60 (0.29), residues: 792 helix: 0.92 (0.26), residues: 395 sheet: 0.21 (0.67), residues: 54 loop : -0.06 (0.33), residues: 343 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 0.016 0.001 PHE D 452 TYR 0.012 0.001 TYR D 515 ARG 0.010 0.001 ARG A 357 *********************** 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 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6747 (mm) REVERT: D 97 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8420 (mm) REVERT: D 161 ARG cc_start: 0.1855 (ttp-170) cc_final: 0.1240 (ttp-170) REVERT: D 219 ARG cc_start: 0.6773 (mtm-85) cc_final: 0.6510 (mtm-85) REVERT: D 290 ASN cc_start: 0.7673 (t0) cc_final: 0.7467 (t0) outliers start: 22 outliers final: 10 residues processed: 84 average time/residue: 0.9694 time to fit residues: 87.0414 Evaluate side-chains 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 364 VAL Chi-restraints excluded: chain D residue 485 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: 2.9990 chunk 75 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.0030 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.140523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.118892 restraints weight = 15167.489| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.68 r_work: 0.3857 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6752 Z= 0.212 Angle : 0.687 14.259 9176 Z= 0.336 Chirality : 0.045 0.219 980 Planarity : 0.004 0.041 1179 Dihedral : 5.194 55.216 1013 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.99 % Allowed : 18.52 % 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: 0.57 (0.29), residues: 792 helix: 0.98 (0.26), residues: 389 sheet: 0.13 (0.67), residues: 54 loop : -0.15 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 275 HIS 0.004 0.001 HIS D 535 PHE 0.028 0.001 PHE D 452 TYR 0.016 0.001 TYR D 158 ARG 0.003 0.000 ARG A 357 *********************** 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 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6818 (mm) REVERT: A 364 ASP cc_start: 0.7105 (t0) cc_final: 0.6771 (t0) REVERT: D 290 ASN cc_start: 0.7675 (t0) cc_final: 0.7473 (t0) outliers start: 21 outliers final: 10 residues processed: 86 average time/residue: 0.9631 time to fit residues: 89.5661 Evaluate side-chains 81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 485 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: 0.0000 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.139615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117966 restraints weight = 15376.474| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.68 r_work: 0.3844 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6752 Z= 0.236 Angle : 0.721 13.855 9176 Z= 0.353 Chirality : 0.047 0.234 980 Planarity : 0.004 0.040 1179 Dihedral : 5.358 56.088 1013 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.56 % Allowed : 19.37 % 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: 0.51 (0.29), residues: 792 helix: 0.89 (0.26), residues: 395 sheet: 0.12 (0.68), residues: 54 loop : -0.15 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 275 HIS 0.004 0.001 HIS D 535 PHE 0.034 0.001 PHE D 452 TYR 0.035 0.001 TYR A 380 ARG 0.006 0.001 ARG D 219 *********************** 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: 18 poor density : 71 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6919 (mm) REVERT: D 161 ARG cc_start: 0.1728 (ttp-170) cc_final: 0.1011 (ttp-170) REVERT: D 273 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7734 (mmm160) REVERT: D 290 ASN cc_start: 0.7709 (t0) cc_final: 0.7500 (t0) outliers start: 18 outliers final: 10 residues processed: 84 average time/residue: 1.0232 time to fit residues: 92.0530 Evaluate side-chains 81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 485 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: 1.9990 chunk 19 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 48 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.141552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.120199 restraints weight = 15300.323| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.66 r_work: 0.3881 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6752 Z= 0.187 Angle : 0.711 13.501 9176 Z= 0.344 Chirality : 0.045 0.203 980 Planarity : 0.004 0.040 1179 Dihedral : 5.020 53.998 1013 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.57 % Allowed : 20.23 % Favored : 78.21 % 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: 1.01 (0.27), residues: 383 sheet: 0.26 (0.68), residues: 54 loop : -0.20 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 275 HIS 0.004 0.001 HIS D 505 PHE 0.026 0.001 PHE D 452 TYR 0.029 0.001 TYR A 380 ARG 0.005 0.000 ARG D 219 ********************** 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 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6902 (mm) REVERT: A 359 SER cc_start: 0.8866 (p) cc_final: 0.8144 (m) REVERT: A 364 ASP cc_start: 0.7181 (t0) cc_final: 0.6861 (t0) REVERT: D 115 ARG cc_start: 0.6138 (tpt-90) cc_final: 0.5620 (ptm-80) REVERT: D 161 ARG cc_start: 0.1785 (ttp-170) cc_final: 0.1109 (ttt180) REVERT: D 290 ASN cc_start: 0.7698 (t0) cc_final: 0.7456 (t0) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 1.0147 time to fit residues: 94.0477 Evaluate side-chains 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 485 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 58 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.141562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.120255 restraints weight = 15461.713| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.69 r_work: 0.3881 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6752 Z= 0.189 Angle : 0.725 13.144 9176 Z= 0.348 Chirality : 0.045 0.191 980 Planarity : 0.004 0.041 1179 Dihedral : 4.936 54.327 1013 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.14 % Allowed : 20.94 % Favored : 77.92 % 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: 0.58 (0.29), residues: 792 helix: 1.01 (0.27), residues: 382 sheet: 0.29 (0.68), residues: 54 loop : -0.17 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 275 HIS 0.004 0.001 HIS D 505 PHE 0.030 0.001 PHE D 452 TYR 0.024 0.001 TYR A 380 ARG 0.005 0.000 ARG D 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4545.65 seconds wall clock time: 81 minutes 26.14 seconds (4886.14 seconds total)