Starting phenix.real_space_refine on Tue Mar 11 16:40:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iup_60911/03_2025/9iup_60911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iup_60911/03_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_60911/03_2025/9iup_60911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iup_60911/03_2025/9iup_60911.map" model { file = "/net/cci-nas-00/data/ceres_data/9iup_60911/03_2025/9iup_60911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iup_60911/03_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-5624/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: 1.56 Conformation dependent library (CDL) restraints added in 901.9 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: 0.63 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: 1.85 Time building geometry restraints manager: 1.84 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- 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 : 0.641 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: 0.1928 time to fit residues: 21.7075 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 : 0.725 ------------------------------------------------------------------------------- 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 = 0.139396 restraints weight = 7177.086| |-----------------------------------------------------------------------------| 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: 0.8151 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 56.048 899 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 : 0.706 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7963 (mmtt) REVERT: A 465 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7366 (ttmm) REVERT: A 482 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8121 (mmm-85) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1755 time to fit residues: 22.2254 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 : 0.702 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 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: 0.4980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.172476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134353 restraints weight = 7260.545| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.42 r_work: 0.3068 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6607 Z= 0.245 Angle : 0.537 6.565 8980 Z= 0.276 Chirality : 0.042 0.212 939 Planarity : 0.004 0.036 1161 Dihedral : 4.317 55.780 899 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: 0.37 (0.31), residues: 783 helix: 1.23 (0.26), residues: 410 sheet: -1.69 (0.78), residues: 54 loop : -0.62 (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 0.014 0.001 PHE A 523 TYR 0.022 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 : 0.658 Fit side-chains REVERT: A 31 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8069 (mmtt) REVERT: A 366 MET cc_start: 0.8026 (tpt) cc_final: 0.7393 (tpp) REVERT: A 465 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7405 (ttmm) REVERT: A 482 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8125 (mmm-85) REVERT: A 489 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: B 394 ASN cc_start: 0.7646 (m-40) cc_final: 0.7380 (m-40) outliers start: 19 outliers final: 12 residues processed: 91 average time/residue: 0.1762 time to fit residues: 22.2423 Evaluate side-chains 87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.0010 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.174106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134099 restraints weight = 7332.267| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.47 r_work: 0.3101 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1179 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= 0.170 Angle : 0.501 6.518 8980 Z= 0.255 Chirality : 0.040 0.197 939 Planarity : 0.003 0.036 1161 Dihedral : 4.141 54.619 899 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.89 % Allowed : 16.47 % Favored : 80.64 % 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: 0.53 (0.31), residues: 783 helix: 1.36 (0.26), residues: 407 sheet: -1.52 (0.79), residues: 54 loop : -0.56 (0.35), residues: 322 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 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8134 (mmtt) REVERT: A 145 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 325 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7174 (tp-100) REVERT: A 366 MET cc_start: 0.8029 (tpt) cc_final: 0.7508 (tpp) REVERT: A 465 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7393 (ttmm) REVERT: A 482 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8088 (mmm-85) REVERT: A 489 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: B 394 ASN cc_start: 0.7609 (m-40) cc_final: 0.7391 (m-40) outliers start: 20 outliers final: 13 residues processed: 96 average time/residue: 0.1874 time to fit residues: 24.4710 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 40.0000 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.174209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135236 restraints weight = 7162.596| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.42 r_work: 0.3098 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1287 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= 0.172 Angle : 0.495 6.788 8980 Z= 0.252 Chirality : 0.040 0.185 939 Planarity : 0.003 0.036 1161 Dihedral : 4.073 54.383 899 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.75 % Allowed : 17.63 % Favored : 79.62 % 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 (0.31), residues: 783 helix: 1.36 (0.26), residues: 410 sheet: -1.42 (0.78), residues: 54 loop : -0.51 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.007 0.001 HIS A 535 PHE 0.012 0.001 PHE A 523 TYR 0.018 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 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8081 (mmtt) REVERT: A 145 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 366 MET cc_start: 0.8026 (tpt) cc_final: 0.7537 (tpp) REVERT: A 465 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7433 (ttmm) REVERT: A 482 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8112 (mmm-85) REVERT: B 394 ASN cc_start: 0.7590 (m-40) cc_final: 0.7335 (m-40) outliers start: 19 outliers final: 13 residues processed: 96 average time/residue: 0.2047 time to fit residues: 27.3159 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 : 0.929 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.201128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158044 restraints weight = 7368.133| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.20 r_work: 0.3360 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6607 Z= 0.257 Angle : 0.544 8.066 8980 Z= 0.275 Chirality : 0.042 0.183 939 Planarity : 0.004 0.036 1161 Dihedral : 4.243 54.555 899 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.32 % Allowed : 17.20 % Favored : 79.48 % 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: 0.45 (0.30), residues: 783 helix: 1.24 (0.26), residues: 410 sheet: -1.47 (0.76), residues: 54 loop : -0.55 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.006 0.001 HIS A 535 PHE 0.013 0.001 PHE A 523 TYR 0.021 0.002 TYR A 385 ARG 0.003 0.000 ARG A 518 *********************** 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 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8177 (mmtt) REVERT: A 145 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 154 ASN cc_start: 0.8810 (p0) cc_final: 0.8474 (p0) REVERT: A 216 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7665 (p0) REVERT: A 293 VAL cc_start: 0.7638 (m) cc_final: 0.7238 (m) REVERT: A 366 MET cc_start: 0.7994 (tpt) cc_final: 0.7433 (tpp) REVERT: A 465 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7489 (ttmm) REVERT: B 394 ASN cc_start: 0.7632 (m-40) cc_final: 0.7404 (m-40) outliers start: 23 outliers final: 18 residues processed: 97 average time/residue: 0.1744 time to fit residues: 23.6912 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 563 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.197983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.159079 restraints weight = 7306.645| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.96 r_work: 0.3402 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6607 Z= 0.194 Angle : 0.508 6.661 8980 Z= 0.259 Chirality : 0.041 0.180 939 Planarity : 0.003 0.037 1161 Dihedral : 4.140 53.896 899 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.61 % Allowed : 18.21 % Favored : 78.18 % 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 (0.30), residues: 783 helix: 1.27 (0.26), residues: 410 sheet: -1.42 (0.74), residues: 54 loop : -0.48 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.006 0.001 HIS A 535 PHE 0.012 0.001 PHE A 523 TYR 0.019 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** 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 109 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8157 (mmtt) REVERT: A 145 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 154 ASN cc_start: 0.8753 (p0) cc_final: 0.8407 (p0) REVERT: A 293 VAL cc_start: 0.7679 (m) cc_final: 0.7067 (m) REVERT: A 366 MET cc_start: 0.7932 (tpt) cc_final: 0.7407 (tpp) REVERT: A 376 MET cc_start: 0.8190 (mmm) cc_final: 0.7935 (mmm) REVERT: A 465 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7508 (ttmm) REVERT: B 394 ASN cc_start: 0.7668 (m-40) cc_final: 0.7429 (m-40) outliers start: 25 outliers final: 19 residues processed: 102 average time/residue: 0.1705 time to fit residues: 24.9574 Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 581 VAL Chi-restraints excluded: chain A residue 599 ASN 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: 0.2980 chunk 48 optimal weight: 0.0970 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.173815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135393 restraints weight = 7251.962| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.29 r_work: 0.3111 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6607 Z= 0.162 Angle : 0.512 7.565 8980 Z= 0.259 Chirality : 0.040 0.175 939 Planarity : 0.003 0.037 1161 Dihedral : 4.076 53.546 899 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.03 % Allowed : 18.79 % Favored : 78.18 % 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: 1.27 (0.26), residues: 410 sheet: -1.23 (0.75), residues: 54 loop : -0.44 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.002 0.000 HIS A 374 PHE 0.012 0.001 PHE A 523 TYR 0.025 0.001 TYR A 279 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 99 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8092 (mmtt) REVERT: A 145 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 154 ASN cc_start: 0.8700 (p0) cc_final: 0.8335 (p0) REVERT: A 293 VAL cc_start: 0.7602 (m) cc_final: 0.7045 (m) REVERT: A 366 MET cc_start: 0.8009 (tpt) cc_final: 0.7471 (tpp) REVERT: A 465 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7412 (ttmm) REVERT: B 394 ASN cc_start: 0.7544 (m-40) cc_final: 0.7280 (m-40) outliers start: 21 outliers final: 17 residues processed: 94 average time/residue: 0.1751 time to fit residues: 22.8828 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.173998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134825 restraints weight = 7307.173| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.37 r_work: 0.3115 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1504 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= 0.174 Angle : 0.522 7.303 8980 Z= 0.264 Chirality : 0.040 0.173 939 Planarity : 0.003 0.037 1161 Dihedral : 4.035 53.377 899 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.75 % Allowed : 19.08 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.31), residues: 783 helix: 1.32 (0.26), residues: 410 sheet: -1.13 (0.77), residues: 54 loop : -0.36 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 302 HIS 0.008 0.001 HIS A 535 PHE 0.012 0.001 PHE A 523 TYR 0.016 0.001 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 97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8695 (p0) cc_final: 0.8330 (p0) REVERT: A 293 VAL cc_start: 0.7628 (m) cc_final: 0.7018 (m) REVERT: A 325 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7161 (tp-100) REVERT: A 366 MET cc_start: 0.8014 (tpt) cc_final: 0.7492 (tpp) REVERT: A 465 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7411 (ttmm) REVERT: A 482 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8257 (mmm-85) REVERT: B 394 ASN cc_start: 0.7508 (m-40) cc_final: 0.7235 (m-40) outliers start: 19 outliers final: 18 residues processed: 92 average time/residue: 0.1601 time to fit residues: 20.6798 Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.173873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134191 restraints weight = 7309.485| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.37 r_work: 0.3111 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1547 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= 0.188 Angle : 0.540 7.835 8980 Z= 0.273 Chirality : 0.041 0.175 939 Planarity : 0.004 0.037 1161 Dihedral : 3.653 17.249 895 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.75 % Allowed : 19.36 % Favored : 77.89 % 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: 0.69 (0.31), residues: 783 helix: 1.34 (0.26), residues: 410 sheet: -1.17 (0.76), residues: 54 loop : -0.33 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 353 HIS 0.012 0.001 HIS A 535 PHE 0.012 0.001 PHE A 523 TYR 0.015 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: 19 poor density : 77 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8679 (p0) cc_final: 0.8323 (p0) REVERT: A 279 TYR cc_start: 0.6954 (t80) cc_final: 0.6654 (t80) REVERT: A 293 VAL cc_start: 0.7642 (m) cc_final: 0.7020 (m) REVERT: A 366 MET cc_start: 0.8007 (tpt) cc_final: 0.7476 (tpp) REVERT: A 465 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7400 (ttmm) REVERT: A 482 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8247 (mmm-85) REVERT: B 394 ASN cc_start: 0.7508 (m-40) cc_final: 0.7222 (m-40) outliers start: 19 outliers final: 18 residues processed: 92 average time/residue: 0.1672 time to fit residues: 21.9262 Evaluate side-chains 92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 297 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.173290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133808 restraints weight = 7470.487| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.50 r_work: 0.3095 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1569 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= 0.192 Angle : 0.546 7.195 8980 Z= 0.277 Chirality : 0.041 0.171 939 Planarity : 0.004 0.037 1161 Dihedral : 3.685 17.759 895 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.89 % Allowed : 19.08 % Favored : 78.03 % 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: 1.36 (0.26), residues: 410 sheet: -1.18 (0.76), residues: 54 loop : -0.35 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 594 HIS 0.003 0.001 HIS A 540 PHE 0.012 0.001 PHE A 523 TYR 0.016 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: 3187.63 seconds wall clock time: 55 minutes 40.71 seconds (3340.71 seconds total)