Starting phenix.real_space_refine on Tue Feb 11 17:10:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iup_60911/02_2025/9iup_60911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iup_60911/02_2025/9iup_60911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iup_60911/02_2025/9iup_60911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iup_60911/02_2025/9iup_60911.map" model { file = "/net/cci-nas-00/data/ceres_data/9iup_60911/02_2025/9iup_60911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iup_60911/02_2025/9iup_60911.cif" } resolution = 3.3 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= 0.002 sd= 0.086 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 4115 2.51 5 N 1064 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 6420 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1547 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.06, per 1000 atoms: 0.63 Number of scatterers: 6420 At special positions: 0 Unit cell: (73.528, 81.608, 118.776, 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 1204 8.00 N 1064 7.00 C 4115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 343 " " NAG B 602 " - " ASN B 354 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 969.5 milliseconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 56.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.531A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.995A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.895A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.621A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.520A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.907A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.823A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.558A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 388 No H-bonds generated for 'chain 'A' and resid 387 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.820A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.508A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.580A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.803A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.967A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.729A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.130A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.502A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.749A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.561A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 314 hydrogen bonds defined for protein. 888 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: 1.78 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1066 1.31 - 1.44: 1927 1.44 - 1.58: 3556 1.58 - 1.72: 0 1.72 - 1.86: 58 Bond restraints: 6607 Sorted by residual: bond pdb=" C PHE A 32 " pdb=" O PHE A 32 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.16e-02 7.43e+03 3.52e+01 bond pdb=" CA ALA A 36 " pdb=" CB ALA A 36 " ideal model delta sigma weight residual 1.528 1.438 0.090 1.59e-02 3.96e+03 3.21e+01 bond pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 1.526 1.457 0.069 1.22e-02 6.72e+03 3.20e+01 bond pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 1.529 1.441 0.089 1.58e-02 4.01e+03 3.14e+01 bond pdb=" CA TYR A 41 " pdb=" C TYR A 41 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.35e-02 5.49e+03 3.11e+01 ... (remaining 6602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 8906 3.41 - 6.81: 65 6.81 - 10.22: 6 10.22 - 13.63: 2 13.63 - 17.04: 1 Bond angle restraints: 8980 Sorted by residual: angle pdb=" C TYR A 41 " pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " ideal model delta sigma weight residual 110.67 93.63 17.04 1.92e+00 2.71e-01 7.87e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 127.41 -13.51 1.80e+00 3.09e-01 5.64e+01 angle pdb=" CA CYS B 379 " pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 114.40 127.64 -13.24 2.30e+00 1.89e-01 3.31e+01 angle pdb=" C HIS A 34 " pdb=" CA HIS A 34 " pdb=" CB HIS A 34 " ideal model delta sigma weight residual 110.96 102.19 8.77 1.54e+00 4.22e-01 3.24e+01 angle pdb=" C ASN A 33 " pdb=" CA ASN A 33 " pdb=" CB ASN A 33 " ideal model delta sigma weight residual 110.84 120.26 -9.42 1.66e+00 3.63e-01 3.22e+01 ... (remaining 8975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 3282 15.94 - 31.88: 455 31.88 - 47.81: 145 47.81 - 63.75: 31 63.75 - 79.69: 13 Dihedral angle restraints: 3926 sinusoidal: 1615 harmonic: 2311 Sorted by residual: dihedral pdb=" C TYR A 41 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " ideal model delta harmonic sigma weight residual -122.60 -102.81 -19.79 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 28.69 64.31 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 155.72 -62.72 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 3923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 812 0.062 - 0.124: 116 0.124 - 0.186: 6 0.186 - 0.248: 2 0.248 - 0.310: 3 Chirality restraints: 939 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA GLU B 493 " pdb=" N GLU B 493 " pdb=" C GLU B 493 " pdb=" CB GLU B 493 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ASN A 33 " pdb=" N ASN A 33 " pdb=" C ASN A 33 " pdb=" CB ASN A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 936 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 495 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C TYR B 495 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR B 495 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 496 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 493 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C GLU B 493 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU B 493 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 494 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 37 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLU A 37 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU A 37 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 38 " 0.014 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 139 2.69 - 3.24: 6180 3.24 - 3.79: 10243 3.79 - 4.35: 13276 4.35 - 4.90: 22740 Nonbonded interactions: 52578 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OD2 ASP A 355 " model vdw 2.176 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.280 3.040 ... (remaining 52573 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: 1.180 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.005 0.090 6607 Z= 0.320 Angle : 0.733 17.037 8980 Z= 0.447 Chirality : 0.046 0.310 939 Planarity : 0.004 0.037 1161 Dihedral : 16.868 79.689 2421 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.14 % Allowed : 19.08 % Favored : 80.78 % Cbeta Deviations : 0.40 % 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 (0.31), residues: 783 helix: 1.40 (0.27), residues: 393 sheet: -1.37 (0.89), residues: 45 loop : -0.57 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.004 0.001 HIS A 34 PHE 0.019 0.001 PHE A 40 TYR 0.038 0.002 TYR B 495 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (mmtt) REVERT: A 325 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7106 (tp-100) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1898 time to fit residues: 21.1626 Evaluate side-chains 79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.176897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.139397 restraints weight = 7177.059| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.33 r_work: 0.3153 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6607 Z= 0.157 Angle : 0.507 7.464 8980 Z= 0.262 Chirality : 0.040 0.233 939 Planarity : 0.004 0.037 1161 Dihedral : 4.251 56.047 899 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.45 % Allowed : 17.05 % Favored : 81.50 % 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 (0.31), residues: 783 helix: 1.38 (0.26), residues: 405 sheet: -1.47 (0.86), residues: 44 loop : -0.55 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 505 PHE 0.012 0.001 PHE A 327 TYR 0.017 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7961 (mmtt) REVERT: A 465 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7365 (ttmm) REVERT: A 482 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8122 (mmm-85) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1883 time to fit residues: 23.6033 Evaluate side-chains 83 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.170711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132594 restraints weight = 7275.077| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.39 r_work: 0.3040 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6607 Z= 0.280 Angle : 0.561 6.907 8980 Z= 0.288 Chirality : 0.042 0.215 939 Planarity : 0.004 0.036 1161 Dihedral : 4.423 55.813 899 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.75 % Allowed : 16.33 % Favored : 80.92 % 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: 0.29 (0.30), residues: 783 helix: 1.16 (0.26), residues: 410 sheet: -1.72 (0.79), residues: 54 loop : -0.65 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 PHE 0.015 0.001 PHE A 523 TYR 0.024 0.002 TYR A 385 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.708 Fit side-chains REVERT: A 31 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8154 (mmtt) REVERT: A 366 MET cc_start: 0.8065 (tpt) cc_final: 0.7408 (tpp) REVERT: A 465 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7418 (ttmm) REVERT: A 482 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8169 (mmm-85) REVERT: A 489 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: B 394 ASN cc_start: 0.7648 (m-40) cc_final: 0.7374 (m-40) outliers start: 19 outliers final: 12 residues processed: 90 average time/residue: 0.1742 time to fit residues: 21.6730 Evaluate side-chains 89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.0070 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.173618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134255 restraints weight = 7328.927| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.53 r_work: 0.3082 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6607 Z= 0.171 Angle : 0.506 6.537 8980 Z= 0.258 Chirality : 0.040 0.199 939 Planarity : 0.003 0.037 1161 Dihedral : 4.188 54.404 899 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.18 % Allowed : 16.47 % Favored : 80.35 % 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: 0.45 (0.31), residues: 783 helix: 1.28 (0.26), residues: 410 sheet: -1.60 (0.79), residues: 54 loop : -0.58 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A 535 PHE 0.011 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8121 (mmtt) REVERT: A 145 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 149 ASN cc_start: 0.7473 (m-40) cc_final: 0.7273 (m-40) REVERT: A 366 MET cc_start: 0.8032 (tpt) cc_final: 0.7502 (tpp) REVERT: A 465 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7358 (ttmm) REVERT: A 482 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.8094 (mmm-85) REVERT: A 489 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: B 394 ASN cc_start: 0.7584 (m-40) cc_final: 0.7360 (m-40) outliers start: 22 outliers final: 14 residues processed: 96 average time/residue: 0.1695 time to fit residues: 22.4278 Evaluate side-chains 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 4 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.176397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137588 restraints weight = 7170.709| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.32 r_work: 0.3140 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6607 Z= 0.141 Angle : 0.478 6.857 8980 Z= 0.243 Chirality : 0.039 0.184 939 Planarity : 0.003 0.037 1161 Dihedral : 3.980 53.817 899 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.89 % Allowed : 17.20 % Favored : 79.91 % 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: 0.68 (0.31), residues: 783 helix: 1.47 (0.26), residues: 407 sheet: -1.45 (0.78), residues: 54 loop : -0.46 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.006 0.001 HIS A 535 PHE 0.012 0.001 PHE A 523 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8040 (mmtt) REVERT: A 145 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 149 ASN cc_start: 0.7520 (m-40) cc_final: 0.7247 (m-40) REVERT: A 216 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7276 (p0) REVERT: A 366 MET cc_start: 0.8001 (tpt) cc_final: 0.7554 (tpp) REVERT: A 465 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7409 (ttmm) REVERT: B 394 ASN cc_start: 0.7525 (m-40) cc_final: 0.7292 (m-40) outliers start: 20 outliers final: 12 residues processed: 101 average time/residue: 0.1771 time to fit residues: 24.3075 Evaluate side-chains 91 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.0010 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.189882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.155834 restraints weight = 7069.517| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.91 r_work: 0.3168 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6607 Z= 0.157 Angle : 0.496 7.957 8980 Z= 0.250 Chirality : 0.040 0.178 939 Planarity : 0.003 0.036 1161 Dihedral : 3.966 53.772 899 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.61 % Allowed : 17.20 % Favored : 79.19 % 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: 0.68 (0.30), residues: 783 helix: 1.45 (0.26), residues: 407 sheet: -1.38 (0.76), residues: 54 loop : -0.45 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.006 0.001 HIS A 535 PHE 0.012 0.001 PHE A 523 TYR 0.020 0.001 TYR A 279 ARG 0.003 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8101 (mmtt) REVERT: A 145 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 149 ASN cc_start: 0.7521 (m-40) cc_final: 0.7195 (m-40) REVERT: A 216 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7421 (p0) REVERT: A 293 VAL cc_start: 0.7526 (m) cc_final: 0.7071 (m) REVERT: A 325 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7156 (tp-100) REVERT: A 366 MET cc_start: 0.8022 (tpt) cc_final: 0.7535 (tpp) REVERT: A 465 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7396 (ttmm) REVERT: B 394 ASN cc_start: 0.7563 (m-40) cc_final: 0.7339 (m-40) outliers start: 25 outliers final: 18 residues processed: 96 average time/residue: 0.1713 time to fit residues: 22.9109 Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.172399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.132769 restraints weight = 7207.922| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.39 r_work: 0.3083 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6607 Z= 0.223 Angle : 0.523 7.158 8980 Z= 0.264 Chirality : 0.041 0.177 939 Planarity : 0.003 0.036 1161 Dihedral : 4.077 53.950 899 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.89 % Allowed : 17.77 % Favored : 79.34 % 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: 0.56 (0.30), residues: 783 helix: 1.33 (0.26), residues: 410 sheet: -1.39 (0.76), residues: 54 loop : -0.49 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 302 HIS 0.005 0.001 HIS A 535 PHE 0.013 0.001 PHE A 523 TYR 0.019 0.002 TYR A 385 ARG 0.003 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8089 (mmtt) REVERT: A 145 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 149 ASN cc_start: 0.7643 (m-40) cc_final: 0.7291 (m-40) REVERT: A 154 ASN cc_start: 0.8783 (p0) cc_final: 0.8449 (p0) REVERT: A 293 VAL cc_start: 0.7557 (m) cc_final: 0.7133 (m) REVERT: A 366 MET cc_start: 0.7987 (tpt) cc_final: 0.7437 (tpp) REVERT: A 465 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7384 (ttmm) REVERT: B 394 ASN cc_start: 0.7497 (m-40) cc_final: 0.7273 (m-40) outliers start: 20 outliers final: 18 residues processed: 93 average time/residue: 0.1609 time to fit residues: 20.8584 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.0030 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7650 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.173958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133590 restraints weight = 7236.711| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.36 r_work: 0.3109 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6607 Z= 0.180 Angle : 0.510 6.945 8980 Z= 0.258 Chirality : 0.040 0.173 939 Planarity : 0.003 0.037 1161 Dihedral : 4.045 53.759 899 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.03 % Allowed : 18.35 % Favored : 78.61 % 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 (0.30), residues: 783 helix: 1.34 (0.26), residues: 410 sheet: -1.39 (0.75), residues: 54 loop : -0.48 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 302 HIS 0.006 0.001 HIS A 535 PHE 0.012 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8189 (mmtt) REVERT: A 145 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 149 ASN cc_start: 0.7625 (m-40) cc_final: 0.7255 (m-40) REVERT: A 154 ASN cc_start: 0.8797 (p0) cc_final: 0.8463 (p0) REVERT: A 293 VAL cc_start: 0.7585 (m) cc_final: 0.7157 (m) REVERT: A 325 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7153 (tp-100) REVERT: A 366 MET cc_start: 0.8058 (tpt) cc_final: 0.7518 (tpp) REVERT: A 465 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7401 (ttmm) REVERT: B 394 ASN cc_start: 0.7560 (m-40) cc_final: 0.7285 (m-40) outliers start: 21 outliers final: 18 residues processed: 96 average time/residue: 0.1796 time to fit residues: 23.4567 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.172442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134169 restraints weight = 7308.160| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.24 r_work: 0.3095 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6607 Z= 0.204 Angle : 0.529 7.355 8980 Z= 0.269 Chirality : 0.041 0.171 939 Planarity : 0.003 0.037 1161 Dihedral : 4.083 53.712 899 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.18 % Allowed : 18.06 % Favored : 78.76 % 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 (0.30), residues: 783 helix: 1.30 (0.26), residues: 410 sheet: -1.24 (0.74), residues: 54 loop : -0.43 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 302 HIS 0.003 0.001 HIS A 540 PHE 0.013 0.001 PHE A 523 TYR 0.019 0.002 TYR A 385 ARG 0.004 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8194 (mmtt) REVERT: A 145 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 149 ASN cc_start: 0.7643 (m-40) cc_final: 0.7256 (m-40) REVERT: A 154 ASN cc_start: 0.8813 (p0) cc_final: 0.8464 (p0) REVERT: A 216 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7474 (p0) REVERT: A 293 VAL cc_start: 0.7620 (m) cc_final: 0.7270 (m) REVERT: A 366 MET cc_start: 0.8046 (tpt) cc_final: 0.7492 (tpp) REVERT: A 465 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7426 (ttmm) REVERT: A 482 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8357 (mmm-85) REVERT: B 394 ASN cc_start: 0.7613 (m-40) cc_final: 0.7333 (m-40) outliers start: 22 outliers final: 19 residues processed: 96 average time/residue: 0.1640 time to fit residues: 21.8623 Evaluate side-chains 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.173007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133205 restraints weight = 7309.306| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.27 r_work: 0.3099 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6607 Z= 0.196 Angle : 0.545 7.922 8980 Z= 0.276 Chirality : 0.041 0.170 939 Planarity : 0.003 0.036 1161 Dihedral : 4.098 53.527 899 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.03 % Allowed : 18.35 % Favored : 78.61 % 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: 0.62 (0.30), residues: 783 helix: 1.31 (0.26), residues: 410 sheet: -1.18 (0.75), residues: 54 loop : -0.40 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 271 HIS 0.002 0.001 HIS A 540 PHE 0.012 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.004 0.000 ARG A 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8102 (mmtt) REVERT: A 145 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 149 ASN cc_start: 0.7688 (m-40) cc_final: 0.7304 (m-40) REVERT: A 154 ASN cc_start: 0.8759 (p0) cc_final: 0.8409 (p0) REVERT: A 216 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7275 (p0) REVERT: A 293 VAL cc_start: 0.7624 (m) cc_final: 0.7047 (m) REVERT: A 325 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7168 (tp-100) REVERT: A 366 MET cc_start: 0.8008 (tpt) cc_final: 0.7492 (tpp) REVERT: A 465 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7402 (ttmm) REVERT: A 482 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.8261 (mmm-85) REVERT: B 394 ASN cc_start: 0.7489 (m-40) cc_final: 0.7206 (m-40) outliers start: 21 outliers final: 18 residues processed: 90 average time/residue: 0.1638 time to fit residues: 20.6808 Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 50.0000 chunk 12 optimal weight: 4.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.173133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134303 restraints weight = 7479.556| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.48 r_work: 0.3097 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6607 Z= 0.188 Angle : 0.534 7.677 8980 Z= 0.270 Chirality : 0.040 0.169 939 Planarity : 0.003 0.036 1161 Dihedral : 4.043 53.277 899 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.75 % Allowed : 18.93 % Favored : 78.32 % 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: 0.61 (0.30), residues: 783 helix: 1.31 (0.26), residues: 410 sheet: -1.26 (0.74), residues: 54 loop : -0.41 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 594 HIS 0.002 0.001 HIS A 540 PHE 0.012 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.004 0.000 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3227.03 seconds wall clock time: 57 minutes 53.72 seconds (3473.72 seconds total)