Starting phenix.real_space_refine on Wed Sep 17 14:22:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqe_60789/09_2025/9iqe_60789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqe_60789/09_2025/9iqe_60789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iqe_60789/09_2025/9iqe_60789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqe_60789/09_2025/9iqe_60789.map" model { file = "/net/cci-nas-00/data/ceres_data/9iqe_60789/09_2025/9iqe_60789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqe_60789/09_2025/9iqe_60789.cif" } resolution = 3.78 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= 0.005 sd= 0.058 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 33 5.16 5 C 5781 2.51 5 N 1612 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9118 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4348 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "B" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4743 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 18, 'TRANS': 600} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.24 Number of scatterers: 9118 At special positions: 0 Unit cell: (70.72, 91.52, 147.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 2 15.00 O 1690 8.00 N 1612 7.00 C 5781 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: 0.86 Conformation dependent library (CDL) restraints added in 353.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 70.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 0 through 10 removed outlier: 4.078A pdb=" N GLN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 45 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 50 through 100 removed outlier: 3.512A pdb=" N THR A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.272A pdb=" N THR A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 153 Processing helix chain 'A' and resid 158 through 203 Proline residue: A 166 - end of helix Proline residue: A 181 - end of helix removed outlier: 3.525A pdb=" N GLY A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 removed outlier: 3.509A pdb=" N PHE A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 240 Processing helix chain 'A' and resid 241 through 267 Processing helix chain 'A' and resid 270 through 293 removed outlier: 4.134A pdb=" N LEU A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 removed outlier: 4.179A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 removed outlier: 4.092A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.800A pdb=" N ALA A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 519 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 32 through 70 Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.707A pdb=" N ARG B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 109 through 158 Processing helix chain 'B' and resid 161 through 168 removed outlier: 4.203A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 removed outlier: 4.120A pdb=" N SER B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 213 removed outlier: 3.590A pdb=" N ASP B 182 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.848A pdb=" N PHE B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 262 removed outlier: 3.561A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 271 through 299 Processing helix chain 'B' and resid 299 through 325 Processing helix chain 'B' and resid 329 through 372 removed outlier: 3.606A pdb=" N ILE B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Proline residue: B 346 - end of helix removed outlier: 4.350A pdb=" N GLN B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.732A pdb=" N ALA B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 493 through 504 removed outlier: 3.605A pdb=" N ILE B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.222A pdb=" N HIS B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 544 Processing helix chain 'B' and resid 559 through 572 Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.573A pdb=" N ILE B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 617 through 627 removed outlier: 3.998A pdb=" N HIS B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 354 removed outlier: 5.868A pdb=" N ALA A 339 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 339 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER A 389 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.379A pdb=" N GLY A 412 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP A 496 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 414 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 368 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP A 543 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 4.082A pdb=" N GLY A 423 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 413 removed outlier: 5.242A pdb=" N LEU B 410 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 470 removed outlier: 6.374A pdb=" N VAL B 470 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 549 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ILE B 582 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 551 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA B 421 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N MET B 598 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL B 423 " --> pdb=" O MET B 598 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP B 599 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1884 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: 1.57 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3080 1.34 - 1.46: 1763 1.46 - 1.58: 4367 1.58 - 1.69: 3 1.69 - 1.81: 61 Bond restraints: 9274 Sorted by residual: bond pdb=" N LEU A 240 " pdb=" CA LEU A 240 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.12e-02 7.97e+03 6.25e+00 bond pdb=" CA SER B 587 " pdb=" CB SER B 587 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.55e-02 4.16e+03 6.23e+00 bond pdb=" N ASP B 61 " pdb=" CA ASP B 61 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" N LEU A 157 " pdb=" CA LEU A 157 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.42e-02 4.96e+03 5.01e+00 bond pdb=" N LEU B 97 " pdb=" CA LEU B 97 " ideal model delta sigma weight residual 1.458 1.486 -0.027 1.27e-02 6.20e+03 4.57e+00 ... (remaining 9269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12363 1.88 - 3.75: 198 3.75 - 5.63: 48 5.63 - 7.50: 16 7.50 - 9.38: 3 Bond angle restraints: 12628 Sorted by residual: angle pdb=" N LEU A 240 " pdb=" CA LEU A 240 " pdb=" C LEU A 240 " ideal model delta sigma weight residual 112.97 107.48 5.49 1.06e+00 8.90e-01 2.68e+01 angle pdb=" C ALA B 554 " pdb=" N THR B 555 " pdb=" CA THR B 555 " ideal model delta sigma weight residual 121.18 130.33 -9.15 1.98e+00 2.55e-01 2.14e+01 angle pdb=" C VAL A 486 " pdb=" N ILE A 487 " pdb=" CA ILE A 487 " ideal model delta sigma weight residual 121.97 114.70 7.27 1.80e+00 3.09e-01 1.63e+01 angle pdb=" CA THR A 36 " pdb=" CB THR A 36 " pdb=" OG1 THR A 36 " ideal model delta sigma weight residual 109.60 103.85 5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" N LEU A 157 " pdb=" CA LEU A 157 " pdb=" C LEU A 157 " ideal model delta sigma weight residual 114.12 109.37 4.75 1.39e+00 5.18e-01 1.17e+01 ... (remaining 12623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.73: 5249 31.73 - 63.45: 248 63.45 - 95.18: 13 95.18 - 126.91: 0 126.91 - 158.63: 1 Dihedral angle restraints: 5511 sinusoidal: 2102 harmonic: 3409 Sorted by residual: dihedral pdb=" C2' ADP B 701 " pdb=" C1' ADP B 701 " pdb=" N9 ADP B 701 " pdb=" C4 ADP B 701 " ideal model delta sinusoidal sigma weight residual 91.55 -67.09 158.63 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CA GLU B 553 " pdb=" C GLU B 553 " pdb=" N ALA B 554 " pdb=" CA ALA B 554 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU B 29 " pdb=" C LEU B 29 " pdb=" N PRO B 30 " pdb=" CA PRO B 30 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1222 0.053 - 0.105: 257 0.105 - 0.158: 35 0.158 - 0.211: 3 0.211 - 0.263: 3 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CG LEU A 445 " pdb=" CB LEU A 445 " pdb=" CD1 LEU A 445 " pdb=" CD2 LEU A 445 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB THR B 191 " pdb=" CA THR B 191 " pdb=" OG1 THR B 191 " pdb=" CG2 THR B 191 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LEU A 240 " pdb=" N LEU A 240 " pdb=" C LEU A 240 " pdb=" CB LEU A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1517 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 415 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 416 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 416 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 416 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 354 " -0.009 2.00e-02 2.50e+03 1.21e-02 2.91e+00 pdb=" CG TYR B 354 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 354 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 354 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 354 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 354 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 354 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 354 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 358 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 359 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " 0.022 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1191 2.75 - 3.29: 9942 3.29 - 3.83: 16075 3.83 - 4.36: 17322 4.36 - 4.90: 30455 Nonbonded interactions: 74985 Sorted by model distance: nonbonded pdb=" O GLN A 270 " pdb=" OG SER A 273 " model vdw 2.213 3.040 nonbonded pdb=" O LEU B 174 " pdb=" OG1 THR B 178 " model vdw 2.230 3.040 nonbonded pdb=" O PHE A 421 " pdb=" ND2 ASN A 428 " model vdw 2.270 3.120 nonbonded pdb=" O SER B 213 " pdb=" OG1 THR B 217 " model vdw 2.274 3.040 nonbonded pdb=" O ASN B 515 " pdb=" OG1 THR B 519 " model vdw 2.295 3.040 ... (remaining 74980 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 : 0.003 0.041 9274 Z= 0.150 Angle : 0.663 9.378 12628 Z= 0.349 Chirality : 0.043 0.263 1520 Planarity : 0.004 0.046 1617 Dihedral : 16.844 158.632 3317 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.78 % Favored : 95.96 % Rotamer: Outliers : 5.12 % Allowed : 24.24 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.25), residues: 1189 helix: 1.46 (0.19), residues: 777 sheet: 0.34 (0.73), residues: 58 loop : -0.17 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 618 TYR 0.030 0.001 TYR B 354 PHE 0.016 0.001 PHE B 336 TRP 0.008 0.001 TRP B 620 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9274) covalent geometry : angle 0.66253 (12628) hydrogen bonds : bond 0.12773 ( 638) hydrogen bonds : angle 5.62541 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8514 (m-80) cc_final: 0.8001 (m-80) REVERT: A 180 MET cc_start: 0.8899 (tpp) cc_final: 0.8660 (mmt) REVERT: A 195 ARG cc_start: 0.7943 (tpp80) cc_final: 0.7498 (tpp80) REVERT: A 215 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 374 LYS cc_start: 0.8904 (pttp) cc_final: 0.8516 (ptpp) REVERT: A 419 TYR cc_start: 0.8676 (t80) cc_final: 0.8398 (t80) REVERT: A 543 ASP cc_start: 0.8538 (t0) cc_final: 0.8287 (t0) REVERT: B 15 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7434 (ptm-80) REVERT: B 160 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 228 LEU cc_start: 0.9309 (mm) cc_final: 0.9048 (mm) REVERT: B 248 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8152 (t0) REVERT: B 281 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: B 353 MET cc_start: 0.7977 (pp-130) cc_final: 0.7484 (ptt) REVERT: B 455 ILE cc_start: 0.8772 (pt) cc_final: 0.8527 (mp) REVERT: B 472 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8445 (tp40) REVERT: B 599 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: B 609 HIS cc_start: 0.8682 (t70) cc_final: 0.8257 (t70) REVERT: B 619 TYR cc_start: 0.9129 (t80) cc_final: 0.8625 (t80) REVERT: B 630 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6096 (mm) outliers start: 49 outliers final: 36 residues processed: 182 average time/residue: 0.0859 time to fit residues: 22.8763 Evaluate side-chains 176 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 158 HIS B 271 HIS B 288 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084750 restraints weight = 19295.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087555 restraints weight = 10840.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089411 restraints weight = 7419.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090453 restraints weight = 5834.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.091337 restraints weight = 5076.386| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9274 Z= 0.279 Angle : 0.703 11.592 12628 Z= 0.359 Chirality : 0.045 0.166 1520 Planarity : 0.005 0.046 1617 Dihedral : 9.695 158.629 1395 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.95 % Favored : 95.88 % Rotamer: Outliers : 8.05 % Allowed : 20.79 % Favored : 71.16 % 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 aren not related in a simple way. whole: 1.26 (0.25), residues: 1189 helix: 1.30 (0.18), residues: 785 sheet: 0.82 (0.75), residues: 53 loop : -0.06 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 212 TYR 0.015 0.002 TYR B 487 PHE 0.021 0.002 PHE B 343 TRP 0.007 0.001 TRP B 246 HIS 0.004 0.002 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 9274) covalent geometry : angle 0.70280 (12628) hydrogen bonds : bond 0.04740 ( 638) hydrogen bonds : angle 4.89322 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 138 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8566 (m-80) cc_final: 0.8002 (m-80) REVERT: A 135 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7557 (mpt) REVERT: A 142 MET cc_start: 0.9102 (tpp) cc_final: 0.8494 (tpp) REVERT: A 195 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7556 (tpp80) REVERT: A 273 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8299 (p) REVERT: A 294 MET cc_start: 0.8169 (mmt) cc_final: 0.7776 (mtt) REVERT: A 419 TYR cc_start: 0.8790 (t80) cc_final: 0.8575 (t80) REVERT: A 478 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8228 (mt0) REVERT: B 15 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7527 (ptm-80) REVERT: B 130 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9274 (mp) REVERT: B 172 GLU cc_start: 0.6812 (tp30) cc_final: 0.6258 (tp30) REVERT: B 228 LEU cc_start: 0.9274 (mm) cc_final: 0.9050 (mm) REVERT: B 310 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8801 (tp) REVERT: B 455 ILE cc_start: 0.8803 (pt) cc_final: 0.8570 (mp) REVERT: B 472 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8421 (tm-30) REVERT: B 599 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: B 619 TYR cc_start: 0.9294 (t80) cc_final: 0.8862 (t80) outliers start: 77 outliers final: 48 residues processed: 198 average time/residue: 0.0768 time to fit residues: 22.8614 Evaluate side-chains 177 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 603 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086359 restraints weight = 19258.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089039 restraints weight = 11263.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090801 restraints weight = 7895.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091712 restraints weight = 6304.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092526 restraints weight = 5533.551| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9274 Z= 0.131 Angle : 0.623 13.556 12628 Z= 0.307 Chirality : 0.043 0.244 1520 Planarity : 0.004 0.046 1617 Dihedral : 8.720 160.779 1369 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 7.00 % Allowed : 22.47 % Favored : 70.53 % 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 aren not related in a simple way. whole: 1.55 (0.25), residues: 1189 helix: 1.62 (0.18), residues: 778 sheet: 0.25 (0.74), residues: 58 loop : -0.05 (0.36), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.011 0.001 TYR A 563 PHE 0.015 0.001 PHE B 343 TRP 0.008 0.001 TRP A 3 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9274) covalent geometry : angle 0.62261 (12628) hydrogen bonds : bond 0.04270 ( 638) hydrogen bonds : angle 4.63109 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 0.364 Fit side-chains REVERT: A 6 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8925 (mp) REVERT: A 9 TYR cc_start: 0.8388 (m-80) cc_final: 0.7846 (m-80) REVERT: A 135 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7677 (mpt) REVERT: A 180 MET cc_start: 0.8796 (tpp) cc_final: 0.8527 (mmt) REVERT: A 195 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7544 (tpp80) REVERT: A 273 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.7911 (p) REVERT: A 294 MET cc_start: 0.8109 (mmt) cc_final: 0.7737 (mtt) REVERT: A 419 TYR cc_start: 0.8620 (t80) cc_final: 0.8403 (t80) REVERT: A 525 ILE cc_start: 0.8951 (mt) cc_final: 0.8737 (pt) REVERT: B 172 GLU cc_start: 0.6712 (tp30) cc_final: 0.6211 (tp30) REVERT: B 248 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8265 (t0) REVERT: B 281 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: B 353 MET cc_start: 0.8080 (ppp) cc_final: 0.7403 (ptm) REVERT: B 472 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 522 ASP cc_start: 0.7457 (t0) cc_final: 0.7006 (t0) REVERT: B 559 ASP cc_start: 0.8018 (p0) cc_final: 0.7799 (p0) REVERT: B 599 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7038 (m-30) outliers start: 67 outliers final: 41 residues processed: 206 average time/residue: 0.0891 time to fit residues: 26.5920 Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 15 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN B 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086646 restraints weight = 19432.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089398 restraints weight = 11356.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091188 restraints weight = 7894.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092154 restraints weight = 6304.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092955 restraints weight = 5529.804| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9274 Z= 0.127 Angle : 0.631 14.291 12628 Z= 0.307 Chirality : 0.043 0.206 1520 Planarity : 0.004 0.047 1617 Dihedral : 8.446 160.206 1358 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 6.27 % Allowed : 24.03 % Favored : 69.70 % 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 aren not related in a simple way. whole: 1.63 (0.25), residues: 1189 helix: 1.71 (0.19), residues: 773 sheet: 0.30 (0.74), residues: 58 loop : -0.05 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 26 TYR 0.020 0.001 TYR B 517 PHE 0.015 0.001 PHE B 343 TRP 0.007 0.001 TRP A 3 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9274) covalent geometry : angle 0.63073 (12628) hydrogen bonds : bond 0.04060 ( 638) hydrogen bonds : angle 4.52692 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 0.355 Fit side-chains REVERT: A 9 TYR cc_start: 0.8384 (m-80) cc_final: 0.7798 (m-80) REVERT: A 135 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7662 (mpt) REVERT: A 180 MET cc_start: 0.8797 (tpp) cc_final: 0.8540 (mmt) REVERT: A 273 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.7830 (p) REVERT: A 285 LEU cc_start: 0.9169 (tt) cc_final: 0.8966 (tp) REVERT: A 294 MET cc_start: 0.8136 (mmt) cc_final: 0.7811 (mtt) REVERT: A 374 LYS cc_start: 0.8494 (pttp) cc_final: 0.8027 (ptpp) REVERT: A 419 TYR cc_start: 0.8537 (t80) cc_final: 0.8326 (t80) REVERT: A 492 ILE cc_start: 0.9153 (mp) cc_final: 0.8888 (mp) REVERT: B 172 GLU cc_start: 0.6782 (tp30) cc_final: 0.6301 (tp30) REVERT: B 248 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8234 (t0) REVERT: B 281 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: B 469 MET cc_start: 0.8969 (ppp) cc_final: 0.8769 (ppp) REVERT: B 472 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 599 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6982 (m-30) outliers start: 60 outliers final: 45 residues processed: 190 average time/residue: 0.0841 time to fit residues: 23.5024 Evaluate side-chains 179 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 129 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 603 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087205 restraints weight = 19425.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089842 restraints weight = 11237.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091585 restraints weight = 7842.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092554 restraints weight = 6260.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093364 restraints weight = 5482.409| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9274 Z= 0.131 Angle : 0.619 13.970 12628 Z= 0.304 Chirality : 0.042 0.194 1520 Planarity : 0.004 0.046 1617 Dihedral : 8.356 159.814 1354 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 6.48 % Allowed : 24.24 % Favored : 69.28 % 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 aren not related in a simple way. whole: 1.56 (0.25), residues: 1189 helix: 1.67 (0.19), residues: 784 sheet: 0.33 (0.73), residues: 58 loop : -0.21 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 26 TYR 0.013 0.001 TYR A 563 PHE 0.015 0.001 PHE B 343 TRP 0.006 0.001 TRP A 3 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9274) covalent geometry : angle 0.61921 (12628) hydrogen bonds : bond 0.03970 ( 638) hydrogen bonds : angle 4.45404 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 0.380 Fit side-chains REVERT: A 6 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9007 (mp) REVERT: A 9 TYR cc_start: 0.8381 (m-80) cc_final: 0.7814 (m-80) REVERT: A 135 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7646 (mpt) REVERT: A 180 MET cc_start: 0.8820 (tpp) cc_final: 0.8572 (mmt) REVERT: A 294 MET cc_start: 0.8154 (mmt) cc_final: 0.7858 (mtt) REVERT: A 374 LYS cc_start: 0.8499 (pttp) cc_final: 0.8024 (ptpp) REVERT: A 419 TYR cc_start: 0.8526 (t80) cc_final: 0.8325 (t80) REVERT: B 172 GLU cc_start: 0.6791 (tp30) cc_final: 0.6306 (tp30) REVERT: B 248 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8195 (t0) REVERT: B 281 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: B 469 MET cc_start: 0.8963 (ppp) cc_final: 0.8709 (ppp) REVERT: B 472 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 599 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.6983 (m-30) outliers start: 62 outliers final: 50 residues processed: 190 average time/residue: 0.0747 time to fit residues: 21.8152 Evaluate side-chains 189 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 603 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 110 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086964 restraints weight = 19343.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089583 restraints weight = 11379.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091273 restraints weight = 8052.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092419 restraints weight = 6467.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092995 restraints weight = 5615.330| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9274 Z= 0.131 Angle : 0.618 12.695 12628 Z= 0.303 Chirality : 0.042 0.186 1520 Planarity : 0.004 0.045 1617 Dihedral : 8.347 160.066 1354 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 6.48 % Allowed : 24.35 % Favored : 69.17 % 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 aren not related in a simple way. whole: 1.56 (0.25), residues: 1189 helix: 1.67 (0.19), residues: 784 sheet: 0.39 (0.73), residues: 58 loop : -0.22 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.010 0.001 TYR B 487 PHE 0.029 0.001 PHE B 509 TRP 0.005 0.001 TRP A 3 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9274) covalent geometry : angle 0.61819 (12628) hydrogen bonds : bond 0.03921 ( 638) hydrogen bonds : angle 4.42128 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9011 (mp) REVERT: A 9 TYR cc_start: 0.8376 (m-80) cc_final: 0.7829 (m-80) REVERT: A 135 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7643 (mpt) REVERT: A 180 MET cc_start: 0.8818 (tpp) cc_final: 0.8580 (mmt) REVERT: A 294 MET cc_start: 0.8147 (mmt) cc_final: 0.7894 (mtt) REVERT: A 419 TYR cc_start: 0.8509 (t80) cc_final: 0.8296 (t80) REVERT: B 172 GLU cc_start: 0.6766 (tp30) cc_final: 0.6300 (tp30) REVERT: B 248 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8187 (t0) REVERT: B 281 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: B 353 MET cc_start: 0.8060 (ppp) cc_final: 0.7525 (ptm) REVERT: B 469 MET cc_start: 0.8949 (ppp) cc_final: 0.8673 (ppp) REVERT: B 472 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8455 (tm-30) REVERT: B 599 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7013 (m-30) REVERT: B 630 ILE cc_start: 0.5566 (OUTLIER) cc_final: 0.5144 (mm) outliers start: 62 outliers final: 50 residues processed: 186 average time/residue: 0.0730 time to fit residues: 21.0262 Evaluate side-chains 193 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 108 optimal weight: 0.0970 chunk 92 optimal weight: 9.9990 chunk 111 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088695 restraints weight = 19206.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091426 restraints weight = 11208.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093220 restraints weight = 7843.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094203 restraints weight = 6241.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095034 restraints weight = 5459.036| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9274 Z= 0.120 Angle : 0.620 14.354 12628 Z= 0.300 Chirality : 0.042 0.185 1520 Planarity : 0.004 0.044 1617 Dihedral : 8.297 160.087 1354 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.45 % Favored : 96.38 % Rotamer: Outliers : 5.64 % Allowed : 25.91 % Favored : 68.44 % 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 aren not related in a simple way. whole: 1.61 (0.25), residues: 1189 helix: 1.71 (0.19), residues: 787 sheet: 0.44 (0.73), residues: 58 loop : -0.24 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.015 0.001 TYR A 563 PHE 0.021 0.001 PHE B 509 TRP 0.006 0.001 TRP A 3 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9274) covalent geometry : angle 0.62024 (12628) hydrogen bonds : bond 0.03828 ( 638) hydrogen bonds : angle 4.35189 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8907 (mp) REVERT: A 9 TYR cc_start: 0.8312 (m-80) cc_final: 0.7834 (m-80) REVERT: A 135 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7612 (mpt) REVERT: A 180 MET cc_start: 0.8794 (tpp) cc_final: 0.8569 (mmt) REVERT: A 195 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7610 (tmm160) REVERT: B 130 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9241 (mp) REVERT: B 172 GLU cc_start: 0.6750 (tp30) cc_final: 0.6330 (tp30) REVERT: B 248 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8112 (t0) REVERT: B 281 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: B 282 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 353 MET cc_start: 0.8078 (ppp) cc_final: 0.7599 (ptm) REVERT: B 469 MET cc_start: 0.8890 (ppp) cc_final: 0.8612 (ppp) REVERT: B 472 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 599 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: B 630 ILE cc_start: 0.5472 (OUTLIER) cc_final: 0.5050 (mm) outliers start: 54 outliers final: 37 residues processed: 201 average time/residue: 0.0799 time to fit residues: 23.7928 Evaluate side-chains 192 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 105 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090054 restraints weight = 19061.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092790 restraints weight = 11084.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094392 restraints weight = 7708.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095594 restraints weight = 6200.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096309 restraints weight = 5372.438| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9274 Z= 0.125 Angle : 0.646 13.304 12628 Z= 0.313 Chirality : 0.043 0.244 1520 Planarity : 0.004 0.058 1617 Dihedral : 8.086 159.620 1350 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 5.85 % Allowed : 25.81 % Favored : 68.34 % 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 aren not related in a simple way. whole: 1.57 (0.25), residues: 1189 helix: 1.68 (0.19), residues: 786 sheet: 0.32 (0.72), residues: 59 loop : -0.22 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.024 0.001 TYR A 419 PHE 0.019 0.001 PHE B 509 TRP 0.005 0.001 TRP A 3 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9274) covalent geometry : angle 0.64574 (12628) hydrogen bonds : bond 0.03855 ( 638) hydrogen bonds : angle 4.35557 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8886 (mp) REVERT: A 9 TYR cc_start: 0.8295 (m-80) cc_final: 0.7813 (m-80) REVERT: A 135 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7607 (mpt) REVERT: A 195 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7633 (tmm160) REVERT: A 374 LYS cc_start: 0.8455 (pttp) cc_final: 0.8038 (ptpp) REVERT: A 419 TYR cc_start: 0.8147 (t80) cc_final: 0.7905 (t80) REVERT: B 17 PHE cc_start: 0.6310 (t80) cc_final: 0.5967 (t80) REVERT: B 172 GLU cc_start: 0.6794 (tp30) cc_final: 0.6359 (tp30) REVERT: B 248 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8096 (t0) REVERT: B 281 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: B 282 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 353 MET cc_start: 0.8094 (ppp) cc_final: 0.7640 (ptm) REVERT: B 469 MET cc_start: 0.8883 (ppp) cc_final: 0.8629 (ppp) REVERT: B 472 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 570 MET cc_start: 0.7806 (ppp) cc_final: 0.7046 (ppp) REVERT: B 599 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: B 630 ILE cc_start: 0.5441 (OUTLIER) cc_final: 0.5039 (mm) outliers start: 56 outliers final: 41 residues processed: 201 average time/residue: 0.0770 time to fit residues: 23.3228 Evaluate side-chains 191 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089564 restraints weight = 19244.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092256 restraints weight = 11140.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094034 restraints weight = 7746.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094922 restraints weight = 6155.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095778 restraints weight = 5397.342| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9274 Z= 0.138 Angle : 0.662 12.723 12628 Z= 0.320 Chirality : 0.043 0.204 1520 Planarity : 0.004 0.057 1617 Dihedral : 7.974 159.253 1348 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 5.85 % Allowed : 26.23 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.25), residues: 1189 helix: 1.60 (0.18), residues: 787 sheet: 0.26 (0.71), residues: 59 loop : -0.20 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 26 TYR 0.019 0.002 TYR A 419 PHE 0.017 0.001 PHE A 472 TRP 0.006 0.001 TRP A 3 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9274) covalent geometry : angle 0.66229 (12628) hydrogen bonds : bond 0.03869 ( 638) hydrogen bonds : angle 4.38508 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8887 (mp) REVERT: A 9 TYR cc_start: 0.8303 (m-80) cc_final: 0.7813 (m-80) REVERT: A 135 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7633 (mpt) REVERT: A 195 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7636 (tmm160) REVERT: A 374 LYS cc_start: 0.8477 (pttp) cc_final: 0.8043 (ptpp) REVERT: A 419 TYR cc_start: 0.8153 (t80) cc_final: 0.7924 (t80) REVERT: B 17 PHE cc_start: 0.6253 (t80) cc_final: 0.5892 (t80) REVERT: B 172 GLU cc_start: 0.6766 (tp30) cc_final: 0.6353 (tp30) REVERT: B 281 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: B 282 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 353 MET cc_start: 0.8152 (ppp) cc_final: 0.7677 (ptt) REVERT: B 469 MET cc_start: 0.8854 (ppp) cc_final: 0.8578 (ppp) REVERT: B 472 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8430 (tm-30) REVERT: B 599 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: B 630 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.4962 (mm) outliers start: 56 outliers final: 40 residues processed: 194 average time/residue: 0.0745 time to fit residues: 21.8734 Evaluate side-chains 195 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087661 restraints weight = 19163.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090142 restraints weight = 11369.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091827 restraints weight = 8123.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092872 restraints weight = 6528.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093402 restraints weight = 5723.530| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9274 Z= 0.173 Angle : 0.711 14.607 12628 Z= 0.341 Chirality : 0.044 0.254 1520 Planarity : 0.004 0.054 1617 Dihedral : 7.857 159.061 1344 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 5.02 % Allowed : 27.59 % Favored : 67.40 % 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 aren not related in a simple way. whole: 1.44 (0.25), residues: 1189 helix: 1.59 (0.19), residues: 783 sheet: 0.18 (0.71), residues: 59 loop : -0.28 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 26 TYR 0.016 0.002 TYR A 419 PHE 0.018 0.002 PHE B 509 TRP 0.005 0.001 TRP B 246 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9274) covalent geometry : angle 0.71085 (12628) hydrogen bonds : bond 0.04033 ( 638) hydrogen bonds : angle 4.48172 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 9 TYR cc_start: 0.8374 (m-80) cc_final: 0.7853 (m-80) REVERT: A 135 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7603 (mpt) REVERT: A 195 ARG cc_start: 0.7841 (ttp-170) cc_final: 0.7629 (tmm160) REVERT: A 374 LYS cc_start: 0.8565 (pttp) cc_final: 0.8158 (pttt) REVERT: B 17 PHE cc_start: 0.6356 (t80) cc_final: 0.5989 (t80) REVERT: B 172 GLU cc_start: 0.6801 (tp30) cc_final: 0.6337 (tp30) REVERT: B 248 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8203 (t0) REVERT: B 281 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: B 469 MET cc_start: 0.8866 (ppp) cc_final: 0.8607 (ppp) REVERT: B 472 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 570 MET cc_start: 0.7773 (ppp) cc_final: 0.7000 (ppp) REVERT: B 599 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6929 (m-30) REVERT: B 630 ILE cc_start: 0.5413 (OUTLIER) cc_final: 0.5000 (mm) outliers start: 48 outliers final: 40 residues processed: 181 average time/residue: 0.0751 time to fit residues: 20.5691 Evaluate side-chains 189 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 630 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088859 restraints weight = 18827.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091683 restraints weight = 10555.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093525 restraints weight = 7221.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094717 restraints weight = 5661.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.095092 restraints weight = 4870.094| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9274 Z= 0.140 Angle : 0.693 14.748 12628 Z= 0.328 Chirality : 0.044 0.262 1520 Planarity : 0.004 0.054 1617 Dihedral : 7.867 159.583 1344 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 5.12 % Allowed : 27.80 % Favored : 67.08 % 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 aren not related in a simple way. whole: 1.52 (0.25), residues: 1189 helix: 1.64 (0.19), residues: 781 sheet: 0.17 (0.72), residues: 59 loop : -0.17 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.028 0.002 TYR A 33 PHE 0.019 0.001 PHE A 472 TRP 0.005 0.001 TRP A 3 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9274) covalent geometry : angle 0.69270 (12628) hydrogen bonds : bond 0.03974 ( 638) hydrogen bonds : angle 4.45053 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1563.75 seconds wall clock time: 27 minutes 51.20 seconds (1671.20 seconds total)