Starting phenix.real_space_refine on Sun May 3 00:18:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zuy_60501/05_2026/8zuy_60501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zuy_60501/05_2026/8zuy_60501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zuy_60501/05_2026/8zuy_60501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zuy_60501/05_2026/8zuy_60501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zuy_60501/05_2026/8zuy_60501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zuy_60501/05_2026/8zuy_60501.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 5743 2.51 5 N 1602 2.21 5 O 1754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9157 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5190 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 24, 'TRANS': 648} Chain: "B" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1906 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "F" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1973 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {' MG': 1, 'ATP': 1, 'BCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'1VU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.08, per 1000 atoms: 0.34 Number of scatterers: 9157 At special positions: 0 Unit cell: (96.6, 98.28, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 1 11.99 O 1754 8.00 N 1602 7.00 C 5743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 367.1 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 14 sheets defined 40.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.856A pdb=" N ALA A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 4.465A pdb=" N SER A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.743A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.518A pdb=" N ILE A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.856A pdb=" N ILE B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 384 removed outlier: 3.573A pdb=" N PHE B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.695A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.794A pdb=" N ASP B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.542A pdb=" N CYS B 448 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 478 through 491 removed outlier: 3.903A pdb=" N ALA B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.635A pdb=" N ARG B 499 " --> pdb=" O PRO B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 522 Processing helix chain 'F' and resid 34 through 49 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 169 through 187 removed outlier: 3.613A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 205 through 211 removed outlier: 3.619A pdb=" N ALA F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 263 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.576A pdb=" N THR A 89 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL A 110 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 91 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 289 removed outlier: 4.650A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR A 334 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET A 350 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 336 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 565 removed outlier: 6.503A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 663 removed outlier: 4.107A pdb=" N VAL A 725 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 695 through 700 removed outlier: 4.276A pdb=" N MET A 699 " --> pdb=" O CYS A 688 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N CYS A 688 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 680 through 681 removed outlier: 3.811A pdb=" N GLY A 705 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.492A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AB5, first strand: chain 'F' and resid 80 through 82 removed outlier: 4.548A pdb=" N THR F 109 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP F 160 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLN F 124 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER F 161 " --> pdb=" O MET F 197 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 198 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1221 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: 1.59 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1561 1.28 - 1.42: 2256 1.42 - 1.56: 5407 1.56 - 1.70: 17 1.70 - 1.84: 82 Bond restraints: 9323 Sorted by residual: bond pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 2.250 1.643 0.607 2.00e-02 2.50e+03 9.20e+02 bond pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " ideal model delta sigma weight residual 1.682 1.467 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C16 1VU F5601 " pdb=" C22 1VU F5601 " ideal model delta sigma weight residual 1.560 1.360 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C16 1VU F5601 " pdb=" O11 1VU F5601 " ideal model delta sigma weight residual 1.425 1.590 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" C15 1VU F5601 " pdb=" O11 1VU F5601 " ideal model delta sigma weight residual 1.459 1.303 0.156 2.00e-02 2.50e+03 6.06e+01 ... (remaining 9318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.19: 12615 11.19 - 22.37: 6 22.37 - 33.56: 3 33.56 - 44.75: 0 44.75 - 55.93: 1 Bond angle restraints: 12625 Sorted by residual: angle pdb=" O14 1VU F5601 " pdb=" P2 1VU F5601 " pdb=" O15 1VU F5601 " ideal model delta sigma weight residual 53.72 109.65 -55.93 3.00e+00 1.11e-01 3.48e+02 angle pdb=" O8 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 140.21 109.19 31.02 3.00e+00 1.11e-01 1.07e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O9 1VU F5601 " ideal model delta sigma weight residual 78.74 109.45 -30.71 3.00e+00 1.11e-01 1.05e+02 angle pdb=" O10 1VU F5601 " pdb=" P1 1VU F5601 " pdb=" O7 1VU F5601 " ideal model delta sigma weight residual 85.76 109.58 -23.82 3.00e+00 1.11e-01 6.30e+01 angle pdb=" P 1VU F5601 " pdb=" O7 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sigma weight residual 143.93 123.94 19.99 3.00e+00 1.11e-01 4.44e+01 ... (remaining 12620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 5591 35.28 - 70.55: 89 70.55 - 105.83: 12 105.83 - 141.11: 0 141.11 - 176.38: 5 Dihedral angle restraints: 5697 sinusoidal: 2314 harmonic: 3383 Sorted by residual: dihedral pdb=" O6 1VU F5601 " pdb=" O7 1VU F5601 " pdb=" P 1VU F5601 " pdb=" P1 1VU F5601 " ideal model delta sinusoidal sigma weight residual -98.95 77.43 -176.38 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C 1VU F5601 " pdb=" C1 1VU F5601 " pdb=" C2 1VU F5601 " pdb=" S 1VU F5601 " ideal model delta sinusoidal sigma weight residual 57.40 -118.11 175.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C 1VU F5601 " pdb=" C1 1VU F5601 " pdb=" C2 1VU F5601 " pdb=" O 1VU F5601 " ideal model delta sinusoidal sigma weight residual 236.12 61.91 174.21 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1409 0.120 - 0.240: 15 0.240 - 0.360: 0 0.360 - 0.480: 0 0.480 - 0.600: 1 Chirality restraints: 1425 Sorted by residual: chirality pdb=" C22 1VU F5601 " pdb=" C16 1VU F5601 " pdb=" C23 1VU F5601 " pdb=" O12 1VU F5601 " both_signs ideal model delta sigma weight residual False -2.99 -2.39 -0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" C16 1VU F5601 " pdb=" C22 1VU F5601 " pdb=" N2 1VU F5601 " pdb=" O11 1VU F5601 " both_signs ideal model delta sigma weight residual False 2.69 2.49 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C15 1VU F5601 " pdb=" C14 1VU F5601 " pdb=" C23 1VU F5601 " pdb=" O11 1VU F5601 " both_signs ideal model delta sigma weight residual False 2.68 2.51 0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 1422 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT A 803 " -0.065 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" O1 BCT A 803 " 0.024 2.00e-02 2.50e+03 pdb=" O2 BCT A 803 " 0.024 2.00e-02 2.50e+03 pdb=" O3 BCT A 803 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 303 " 0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 304 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 473 " 0.014 2.00e-02 2.50e+03 1.15e-02 2.63e+00 pdb=" CG TYR A 473 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 473 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 473 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 473 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 473 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 473 " 0.001 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 103 2.64 - 3.20: 8194 3.20 - 3.77: 13751 3.77 - 4.33: 19780 4.33 - 4.90: 32603 Nonbonded interactions: 74431 Sorted by model distance: nonbonded pdb=" OE1 GLU A 349 " pdb="MG MG A 802 " model vdw 2.073 2.170 nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 802 " model vdw 2.088 2.170 nonbonded pdb=" O1A ATP A 801 " pdb="MG MG A 802 " model vdw 2.183 2.170 nonbonded pdb=" OE2 GLU A 73 " pdb=" OH TYR A 143 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG A 77 " pdb=" OG1 THR A 81 " model vdw 2.283 3.120 ... (remaining 74426 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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 : 0.009 0.607 9323 Z= 0.446 Angle : 0.954 55.932 12625 Z= 0.387 Chirality : 0.047 0.600 1425 Planarity : 0.004 0.052 1640 Dihedral : 14.926 176.384 3521 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1175 helix: 0.97 (0.26), residues: 430 sheet: 0.71 (0.33), residues: 242 loop : -0.69 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 499 TYR 0.028 0.001 TYR A 473 PHE 0.011 0.001 PHE A 629 TRP 0.027 0.002 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00900 ( 9323) covalent geometry : angle 0.95424 (12625) hydrogen bonds : bond 0.15340 ( 441) hydrogen bonds : angle 6.22819 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.374 Fit side-chains REVERT: A 160 ASP cc_start: 0.7035 (t0) cc_final: 0.6638 (t0) REVERT: A 230 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7644 (mtm110) REVERT: A 666 MET cc_start: 0.6087 (ptm) cc_final: 0.5713 (ptm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.8461 time to fit residues: 94.0148 Evaluate side-chains 87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.078168 restraints weight = 13759.263| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.52 r_work: 0.2782 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9323 Z= 0.144 Angle : 0.551 6.295 12625 Z= 0.291 Chirality : 0.045 0.155 1425 Planarity : 0.004 0.052 1640 Dihedral : 13.734 176.514 1373 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.92 % Allowed : 6.74 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1175 helix: 1.25 (0.26), residues: 437 sheet: 0.74 (0.32), residues: 250 loop : -0.60 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 154 TYR 0.023 0.001 TYR A 473 PHE 0.016 0.001 PHE A 242 TRP 0.013 0.001 TRP A 394 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9323) covalent geometry : angle 0.55118 (12625) hydrogen bonds : bond 0.04694 ( 441) hydrogen bonds : angle 4.71480 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 160 ASP cc_start: 0.8070 (t0) cc_final: 0.7603 (t0) REVERT: A 230 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7914 (mtm110) outliers start: 9 outliers final: 2 residues processed: 103 average time/residue: 0.8301 time to fit residues: 89.9247 Evaluate side-chains 89 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 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 149 ASN F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.078749 restraints weight = 13731.086| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.43 r_work: 0.2795 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9323 Z= 0.128 Angle : 0.522 7.968 12625 Z= 0.275 Chirality : 0.044 0.148 1425 Planarity : 0.004 0.045 1640 Dihedral : 12.526 170.852 1373 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.02 % Allowed : 9.09 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1175 helix: 1.44 (0.26), residues: 435 sheet: 0.82 (0.33), residues: 245 loop : -0.62 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.019 0.001 TYR A 473 PHE 0.011 0.001 PHE A 629 TRP 0.009 0.001 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9323) covalent geometry : angle 0.52215 (12625) hydrogen bonds : bond 0.04222 ( 441) hydrogen bonds : angle 4.42972 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 160 ASP cc_start: 0.8126 (t0) cc_final: 0.7655 (t0) REVERT: B 448 CYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8920 (t) REVERT: F 47 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7600 (mt) outliers start: 10 outliers final: 3 residues processed: 99 average time/residue: 0.8367 time to fit residues: 86.8514 Evaluate side-chains 92 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 472 ASN F 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.078739 restraints weight = 13927.064| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.43 r_work: 0.2779 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9323 Z= 0.133 Angle : 0.515 6.117 12625 Z= 0.273 Chirality : 0.044 0.139 1425 Planarity : 0.004 0.048 1640 Dihedral : 11.928 165.070 1373 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.53 % Allowed : 10.11 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1175 helix: 1.53 (0.26), residues: 434 sheet: 0.83 (0.33), residues: 245 loop : -0.60 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.018 0.001 TYR A 473 PHE 0.020 0.001 PHE A 242 TRP 0.008 0.001 TRP A 394 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9323) covalent geometry : angle 0.51456 (12625) hydrogen bonds : bond 0.04139 ( 441) hydrogen bonds : angle 4.33186 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8340 (tptp) cc_final: 0.8104 (tptp) REVERT: A 160 ASP cc_start: 0.8118 (t0) cc_final: 0.7624 (t0) REVERT: A 230 ARG cc_start: 0.8296 (mtm180) cc_final: 0.7988 (mtm110) REVERT: B 433 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (pttp) REVERT: B 448 CYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8945 (t) REVERT: F 47 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7618 (mt) REVERT: F 60 LYS cc_start: 0.8790 (ttpp) cc_final: 0.8456 (tttm) outliers start: 15 outliers final: 5 residues processed: 98 average time/residue: 0.8602 time to fit residues: 88.4375 Evaluate side-chains 93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 147 GLN F 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079089 restraints weight = 13804.758| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.54 r_work: 0.2803 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9323 Z= 0.115 Angle : 0.503 6.203 12625 Z= 0.265 Chirality : 0.043 0.154 1425 Planarity : 0.004 0.045 1640 Dihedral : 11.423 155.977 1373 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.43 % Allowed : 10.83 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1175 helix: 1.56 (0.26), residues: 434 sheet: 0.83 (0.33), residues: 245 loop : -0.56 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 390 TYR 0.014 0.001 TYR A 473 PHE 0.021 0.001 PHE A 242 TRP 0.006 0.001 TRP A 596 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9323) covalent geometry : angle 0.50261 (12625) hydrogen bonds : bond 0.03837 ( 441) hydrogen bonds : angle 4.24355 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.273 Fit side-chains REVERT: A 61 LYS cc_start: 0.8325 (tptp) cc_final: 0.8058 (tptp) REVERT: A 160 ASP cc_start: 0.8104 (t0) cc_final: 0.7604 (t0) REVERT: A 230 ARG cc_start: 0.8354 (mtm180) cc_final: 0.8050 (mtm110) REVERT: A 350 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8592 (ttt) REVERT: B 433 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8418 (pttp) REVERT: B 448 CYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8950 (t) REVERT: F 60 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8455 (tttm) outliers start: 14 outliers final: 6 residues processed: 97 average time/residue: 0.8443 time to fit residues: 85.9297 Evaluate side-chains 93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain F residue 248 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.0030 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 40.0000 chunk 39 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 147 GLN F 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078373 restraints weight = 13783.475| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.41 r_work: 0.2794 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9323 Z= 0.130 Angle : 0.523 7.985 12625 Z= 0.273 Chirality : 0.044 0.152 1425 Planarity : 0.004 0.048 1640 Dihedral : 10.920 140.893 1373 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.33 % Allowed : 11.85 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1175 helix: 1.54 (0.26), residues: 434 sheet: 0.96 (0.33), residues: 235 loop : -0.63 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 390 TYR 0.013 0.001 TYR A 473 PHE 0.032 0.001 PHE A 263 TRP 0.006 0.001 TRP A 596 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9323) covalent geometry : angle 0.52255 (12625) hydrogen bonds : bond 0.04029 ( 441) hydrogen bonds : angle 4.23268 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.377 Fit side-chains REVERT: A 61 LYS cc_start: 0.8315 (tptp) cc_final: 0.8028 (tptp) REVERT: A 160 ASP cc_start: 0.8118 (t0) cc_final: 0.7610 (t0) REVERT: A 230 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8008 (mtm110) REVERT: A 350 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8576 (ttt) REVERT: B 433 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8449 (pttp) REVERT: B 448 CYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8965 (t) REVERT: F 60 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8435 (tttm) outliers start: 13 outliers final: 5 residues processed: 94 average time/residue: 0.8508 time to fit residues: 84.0924 Evaluate side-chains 91 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 448 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 50.0000 chunk 113 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 0.0070 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 147 GLN F 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.078482 restraints weight = 13842.108| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.55 r_work: 0.2781 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9323 Z= 0.134 Angle : 0.523 6.555 12625 Z= 0.275 Chirality : 0.044 0.148 1425 Planarity : 0.004 0.045 1640 Dihedral : 10.330 121.044 1373 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.53 % Allowed : 11.54 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1175 helix: 1.53 (0.26), residues: 434 sheet: 0.96 (0.33), residues: 235 loop : -0.64 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.013 0.001 TYR A 473 PHE 0.031 0.001 PHE A 263 TRP 0.006 0.001 TRP A 596 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9323) covalent geometry : angle 0.52317 (12625) hydrogen bonds : bond 0.04068 ( 441) hydrogen bonds : angle 4.21827 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.413 Fit side-chains REVERT: A 61 LYS cc_start: 0.8324 (tptp) cc_final: 0.8039 (tptp) REVERT: A 160 ASP cc_start: 0.8086 (t0) cc_final: 0.7575 (t0) REVERT: A 230 ARG cc_start: 0.8286 (mtm180) cc_final: 0.8000 (mtm110) REVERT: A 350 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8571 (ttt) REVERT: B 448 CYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8955 (t) REVERT: F 60 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8414 (tttm) outliers start: 15 outliers final: 5 residues processed: 97 average time/residue: 0.8293 time to fit residues: 84.5807 Evaluate side-chains 93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 95 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.077622 restraints weight = 13727.009| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.35 r_work: 0.2779 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9323 Z= 0.141 Angle : 0.539 7.425 12625 Z= 0.282 Chirality : 0.044 0.146 1425 Planarity : 0.004 0.054 1640 Dihedral : 9.726 115.115 1373 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.12 % Allowed : 13.07 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1175 helix: 1.48 (0.26), residues: 435 sheet: 0.95 (0.33), residues: 235 loop : -0.62 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 390 TYR 0.013 0.001 TYR A 473 PHE 0.033 0.002 PHE A 242 TRP 0.006 0.001 TRP A 596 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9323) covalent geometry : angle 0.53947 (12625) hydrogen bonds : bond 0.04145 ( 441) hydrogen bonds : angle 4.23914 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.289 Fit side-chains REVERT: A 61 LYS cc_start: 0.8333 (tptp) cc_final: 0.8069 (tptp) REVERT: A 124 MET cc_start: 0.8481 (mtt) cc_final: 0.8272 (mtp) REVERT: A 160 ASP cc_start: 0.8085 (t0) cc_final: 0.7569 (t0) REVERT: A 230 ARG cc_start: 0.8317 (mtm180) cc_final: 0.8016 (mtm110) REVERT: A 350 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8568 (ttt) REVERT: B 448 CYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8949 (t) outliers start: 11 outliers final: 5 residues processed: 95 average time/residue: 0.8455 time to fit residues: 84.2152 Evaluate side-chains 93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 50.0000 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 66 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.125656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.074883 restraints weight = 13902.612| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.39 r_work: 0.2722 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9323 Z= 0.271 Angle : 0.619 8.085 12625 Z= 0.327 Chirality : 0.048 0.150 1425 Planarity : 0.005 0.067 1640 Dihedral : 9.413 114.214 1373 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.23 % Allowed : 13.28 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1175 helix: 1.30 (0.26), residues: 434 sheet: 1.00 (0.33), residues: 235 loop : -0.72 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 390 TYR 0.018 0.002 TYR B 417 PHE 0.035 0.002 PHE A 242 TRP 0.010 0.002 TRP B 531 HIS 0.008 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 9323) covalent geometry : angle 0.61950 (12625) hydrogen bonds : bond 0.05381 ( 441) hydrogen bonds : angle 4.44211 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.473 Fit side-chains REVERT: A 61 LYS cc_start: 0.8327 (tptp) cc_final: 0.8044 (tptp) REVERT: A 160 ASP cc_start: 0.8109 (t0) cc_final: 0.7563 (t0) REVERT: A 230 ARG cc_start: 0.8328 (mtm180) cc_final: 0.8052 (mtm110) REVERT: A 350 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8661 (ttt) outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 0.8525 time to fit residues: 84.3078 Evaluate side-chains 93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain F residue 144 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.077552 restraints weight = 13691.375| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.36 r_work: 0.2784 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9323 Z= 0.127 Angle : 0.557 8.583 12625 Z= 0.291 Chirality : 0.044 0.151 1425 Planarity : 0.004 0.063 1640 Dihedral : 9.129 112.066 1373 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.82 % Allowed : 13.69 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1175 helix: 1.42 (0.26), residues: 435 sheet: 0.95 (0.33), residues: 229 loop : -0.70 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 390 TYR 0.013 0.001 TYR A 473 PHE 0.037 0.001 PHE A 242 TRP 0.007 0.001 TRP A 596 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9323) covalent geometry : angle 0.55723 (12625) hydrogen bonds : bond 0.04003 ( 441) hydrogen bonds : angle 4.27671 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.288 Fit side-chains REVERT: A 61 LYS cc_start: 0.8331 (tptp) cc_final: 0.8111 (tptp) REVERT: A 160 ASP cc_start: 0.8114 (t0) cc_final: 0.7601 (t0) REVERT: A 230 ARG cc_start: 0.8314 (mtm180) cc_final: 0.8053 (mtm110) REVERT: A 350 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8602 (ttt) REVERT: B 448 CYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8951 (t) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.8524 time to fit residues: 80.3630 Evaluate side-chains 93 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 448 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.0020 chunk 104 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 overall best weight: 0.2986 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.080154 restraints weight = 13631.391| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.34 r_work: 0.2830 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9323 Z= 0.099 Angle : 0.526 8.810 12625 Z= 0.274 Chirality : 0.043 0.152 1425 Planarity : 0.004 0.062 1640 Dihedral : 8.906 113.139 1373 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.92 % Allowed : 13.38 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1175 helix: 1.57 (0.26), residues: 435 sheet: 0.91 (0.33), residues: 229 loop : -0.62 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 390 TYR 0.008 0.001 TYR A 473 PHE 0.037 0.001 PHE A 242 TRP 0.009 0.001 TRP A 596 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9323) covalent geometry : angle 0.52558 (12625) hydrogen bonds : bond 0.03359 ( 441) hydrogen bonds : angle 4.14814 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4684.21 seconds wall clock time: 80 minutes 14.33 seconds (4814.33 seconds total)