Starting phenix.real_space_refine on Wed Jul 1 23:28:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnb_34909/07_2026/8hnb_34909.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 2689 2.51 5 N 649 2.21 5 O 713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4083 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4041 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 3 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'HIS:plan': 4, 'ARG:plan': 6, 'TYR:plan': 7, 'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 10, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.79, per 1000 atoms: 0.19 Number of scatterers: 4083 At special positions: 0 Unit cell: (101.504, 59.072, 79.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 713 8.00 N 649 7.00 C 2689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.04 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.04 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 144.8 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 69.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 26 through 60 removed outlier: 4.140A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 removed outlier: 3.900A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.794A pdb=" N LEU A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.588A pdb=" N MET A 118 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.546A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.596A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.971A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.782A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.516A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.923A pdb=" N PHE A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 335 through 366 removed outlier: 5.212A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 401 removed outlier: 3.846A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.571A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.131A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.515A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 3.710A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.597A pdb=" N LEU A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 removed outlier: 4.442A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.594A pdb=" N PHE A 501 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER A 492 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 503 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 602 removed outlier: 7.059A pdb=" N THR A 615 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP A 602 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS A 613 " --> pdb=" O TRP A 602 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 768 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: 0.60 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 744 1.33 - 1.45: 1084 1.45 - 1.57: 2302 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 4178 Sorted by residual: bond pdb=" C4 NAG B 1 " pdb=" O4 NAG B 1 " ideal model delta sigma weight residual 1.409 1.481 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA ALA A 581 " pdb=" C ALA A 581 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.75e+00 bond pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 1.520 1.557 -0.037 1.26e-02 6.30e+03 8.62e+00 bond pdb=" C GLN A 369 " pdb=" N PRO A 370 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.23e+00 bond pdb=" C TYR A 640 " pdb=" O TYR A 640 " ideal model delta sigma weight residual 1.236 1.205 0.032 1.15e-02 7.56e+03 7.57e+00 ... (remaining 4173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 5330 2.65 - 5.30: 293 5.30 - 7.94: 45 7.94 - 10.59: 6 10.59 - 13.24: 2 Bond angle restraints: 5676 Sorted by residual: angle pdb=" N TYR A 121 " pdb=" CA TYR A 121 " pdb=" C TYR A 121 " ideal model delta sigma weight residual 109.15 98.24 10.91 1.44e+00 4.82e-01 5.74e+01 angle pdb=" N PHE A 591 " pdb=" CA PHE A 591 " pdb=" C PHE A 591 " ideal model delta sigma weight residual 111.14 104.03 7.11 1.08e+00 8.57e-01 4.33e+01 angle pdb=" N GLU A 364 " pdb=" CA GLU A 364 " pdb=" C GLU A 364 " ideal model delta sigma weight residual 111.36 118.51 -7.15 1.09e+00 8.42e-01 4.30e+01 angle pdb=" N LEU A 113 " pdb=" CA LEU A 113 " pdb=" C LEU A 113 " ideal model delta sigma weight residual 109.81 123.05 -13.24 2.21e+00 2.05e-01 3.59e+01 angle pdb=" N TYR A 502 " pdb=" CA TYR A 502 " pdb=" C TYR A 502 " ideal model delta sigma weight residual 110.42 119.66 -9.24 1.55e+00 4.16e-01 3.55e+01 ... (remaining 5671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 2147 14.03 - 28.06: 182 28.06 - 42.08: 58 42.08 - 56.11: 10 56.11 - 70.13: 2 Dihedral angle restraints: 2399 sinusoidal: 798 harmonic: 1601 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -129.16 43.16 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" N ILE A 407 " pdb=" C ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual 123.40 135.31 -11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" C ILE A 407 " pdb=" N ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual -122.00 -133.65 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 2396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 523 0.083 - 0.166: 114 0.166 - 0.249: 23 0.249 - 0.332: 8 0.332 - 0.415: 5 Chirality restraints: 673 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA SER A 140 " pdb=" N SER A 140 " pdb=" C SER A 140 " pdb=" CB SER A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 670 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.290 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG A 701 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.140 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG B 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.113 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 1748 2.89 - 3.39: 4409 3.39 - 3.89: 6500 3.89 - 4.40: 7456 4.40 - 4.90: 12134 Nonbonded interactions: 32247 Sorted by model distance: nonbonded pdb=" O SER A 140 " pdb=" N CYS A 485 " model vdw 2.382 3.120 nonbonded pdb=" O3 NAG B 1 " pdb=" O5 NAG B 2 " model vdw 2.455 3.040 nonbonded pdb=" OG SER A 328 " pdb=" CD2 LEU A 570 " model vdw 2.458 3.460 nonbonded pdb=" N GLY A 223 " pdb=" N PHE A 224 " model vdw 2.460 2.560 nonbonded pdb=" N SER A 457 " pdb=" O SER A 457 " model vdw 2.496 2.496 ... (remaining 32242 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.500 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.008 0.209 4188 Z= 0.513 Angle : 1.390 13.985 5699 Z= 0.925 Chirality : 0.083 0.415 673 Planarity : 0.016 0.261 698 Dihedral : 12.001 70.135 1358 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.09 % Allowed : 9.92 % Favored : 87.99 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.33), residues: 554 helix: 0.20 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.025 0.002 TYR A 338 PHE 0.014 0.001 PHE A 574 TRP 0.019 0.002 TRP A 259 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.48 ( 4178) covalent geometry : angle 1.34865 / 0.92 ( 5676) SS BOND : bond 0.00758 / 0.37 ( 7) SS BOND : angle 1.49258 / 1.16 ( 14) hydrogen bonds : bond 0.22210 / 15.54 ( 259) hydrogen bonds : angle 8.19178 / 6.24 ( 768) link_BETA1-4 : bond 0.04861 / 2.56 ( 1) link_BETA1-4 : angle 9.14291 / 5.05 ( 3) link_NAG-ASN : bond 0.15224 / 7.29 ( 2) link_NAG-ASN : angle 8.27917 / 5.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.140 Fit side-chains REVERT: A 48 MET cc_start: 0.8622 (tpt) cc_final: 0.8343 (tpt) REVERT: A 115 HIS cc_start: 0.7412 (t-90) cc_final: 0.7126 (t-90) REVERT: A 332 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6262 (mm) outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 0.0683 time to fit residues: 10.4367 Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.233363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.179712 restraints weight = 4501.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184124 restraints weight = 2659.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186399 restraints weight = 1929.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.188294 restraints weight = 1616.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.189024 restraints weight = 1449.316| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4188 Z= 0.170 Angle : 0.765 12.331 5699 Z= 0.364 Chirality : 0.044 0.297 673 Planarity : 0.004 0.030 698 Dihedral : 4.027 15.283 593 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.61 % Allowed : 16.97 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.34), residues: 554 helix: 1.22 (0.27), residues: 332 sheet: -5.41 (0.49), residues: 5 loop : -1.16 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 532 TYR 0.020 0.002 TYR A 338 PHE 0.016 0.001 PHE A 73 TRP 0.013 0.001 TRP A 171 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 4178) covalent geometry : angle 0.73774 / 0.36 ( 5676) SS BOND : bond 0.00277 / 0.13 ( 7) SS BOND : angle 0.92958 / 0.81 ( 14) hydrogen bonds : bond 0.05817 / 3.74 ( 259) hydrogen bonds : angle 5.12976 / 3.87 ( 768) link_BETA1-4 : bond 0.00897 / 0.47 ( 1) link_BETA1-4 : angle 2.29980 / 1.23 ( 3) link_NAG-ASN : bond 0.01785 / 0.93 ( 2) link_NAG-ASN : angle 6.06234 / 4.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 57 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8269 (mtp180) REVERT: A 251 ASP cc_start: 0.7285 (t0) cc_final: 0.6960 (t0) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.0673 time to fit residues: 8.7891 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 115 HIS ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.234186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180780 restraints weight = 4469.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.185152 restraints weight = 2609.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.187527 restraints weight = 1888.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189386 restraints weight = 1577.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.189690 restraints weight = 1408.094| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4188 Z= 0.147 Angle : 0.703 12.168 5699 Z= 0.332 Chirality : 0.042 0.280 673 Planarity : 0.004 0.031 698 Dihedral : 3.731 12.898 591 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.70 % Allowed : 18.80 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.35), residues: 554 helix: 1.46 (0.27), residues: 344 sheet: None (None), residues: 0 loop : -0.69 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 532 TYR 0.040 0.002 TYR A 590 PHE 0.012 0.001 PHE A 73 TRP 0.007 0.001 TRP A 171 HIS 0.016 0.003 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 4178) covalent geometry : angle 0.67624 / 0.33 ( 5676) SS BOND : bond 0.00197 / 0.10 ( 7) SS BOND : angle 0.87127 / 0.71 ( 14) hydrogen bonds : bond 0.04984 / 3.28 ( 259) hydrogen bonds : angle 4.73086 / 3.57 ( 768) link_BETA1-4 : bond 0.00400 / 0.21 ( 1) link_BETA1-4 : angle 1.29967 / 0.91 ( 3) link_NAG-ASN : bond 0.01490 / 0.78 ( 2) link_NAG-ASN : angle 5.87797 / 3.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: A 27 LEU cc_start: 0.7176 (tt) cc_final: 0.6668 (tt) REVERT: A 48 MET cc_start: 0.8825 (tpt) cc_final: 0.8544 (tpt) REVERT: A 580 ARG cc_start: 0.7150 (ttp-110) cc_final: 0.6831 (ttm-80) outliers start: 18 outliers final: 8 residues processed: 102 average time/residue: 0.0600 time to fit residues: 7.6387 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.0060 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 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 = 0.4196 r_free = 0.4196 target = 0.191556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132164 restraints weight = 4807.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137827 restraints weight = 2342.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141455 restraints weight = 1503.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143439 restraints weight = 1157.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144902 restraints weight = 1001.179| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4188 Z= 0.149 Angle : 0.705 12.129 5699 Z= 0.333 Chirality : 0.042 0.278 673 Planarity : 0.004 0.035 698 Dihedral : 3.665 12.319 591 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.18 % Allowed : 20.10 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.35), residues: 554 helix: 1.59 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.80 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 532 TYR 0.045 0.002 TYR A 590 PHE 0.013 0.001 PHE A 73 TRP 0.013 0.002 TRP A 470 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 4178) covalent geometry : angle 0.67780 / 0.33 ( 5676) SS BOND : bond 0.00220 / 0.11 ( 7) SS BOND : angle 1.00217 / 0.81 ( 14) hydrogen bonds : bond 0.04679 / 3.08 ( 259) hydrogen bonds : angle 4.47700 / 3.37 ( 768) link_BETA1-4 : bond 0.00319 / 0.17 ( 1) link_BETA1-4 : angle 0.96491 / 0.65 ( 3) link_NAG-ASN : bond 0.01370 / 0.72 ( 2) link_NAG-ASN : angle 5.90752 / 3.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.093 Fit side-chains REVERT: A 27 LEU cc_start: 0.6474 (tt) cc_final: 0.6046 (tt) REVERT: A 117 PHE cc_start: 0.8332 (m-10) cc_final: 0.8082 (m-10) REVERT: A 198 ASP cc_start: 0.7966 (m-30) cc_final: 0.7741 (m-30) REVERT: A 580 ARG cc_start: 0.6758 (ttp-110) cc_final: 0.6547 (mtp-110) outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 0.0683 time to fit residues: 8.6617 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 20 optimal weight: 0.0770 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 178 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 = 0.4201 r_free = 0.4201 target = 0.192037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133379 restraints weight = 4758.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139056 restraints weight = 2299.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142700 restraints weight = 1472.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144714 restraints weight = 1124.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146211 restraints weight = 968.638| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4188 Z= 0.140 Angle : 0.689 12.153 5699 Z= 0.321 Chirality : 0.042 0.264 673 Planarity : 0.004 0.042 698 Dihedral : 3.575 11.348 591 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.18 % Allowed : 20.10 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.35), residues: 554 helix: 1.69 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 532 TYR 0.038 0.002 TYR A 590 PHE 0.013 0.001 PHE A 73 TRP 0.012 0.001 TRP A 470 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4178) covalent geometry : angle 0.66182 / 0.31 ( 5676) SS BOND : bond 0.00102 / 0.05 ( 7) SS BOND : angle 0.82039 / 0.65 ( 14) hydrogen bonds : bond 0.04516 / 2.98 ( 259) hydrogen bonds : angle 4.38852 / 3.29 ( 768) link_BETA1-4 : bond 0.00138 / 0.07 ( 1) link_BETA1-4 : angle 0.81103 / 0.58 ( 3) link_NAG-ASN : bond 0.01315 / 0.69 ( 2) link_NAG-ASN : angle 5.93437 / 3.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.152 Fit side-chains REVERT: A 27 LEU cc_start: 0.6487 (tt) cc_final: 0.6021 (tt) REVERT: A 580 ARG cc_start: 0.6726 (ttp-110) cc_final: 0.6194 (ttm-80) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.0745 time to fit residues: 8.9434 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 28 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 178 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 = 0.4193 r_free = 0.4193 target = 0.190544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131535 restraints weight = 4851.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137173 restraints weight = 2370.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140840 restraints weight = 1531.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142600 restraints weight = 1174.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144193 restraints weight = 1021.133| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4188 Z= 0.146 Angle : 0.701 12.161 5699 Z= 0.324 Chirality : 0.042 0.262 673 Planarity : 0.004 0.047 698 Dihedral : 3.523 13.716 591 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.92 % Allowed : 20.37 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.35), residues: 554 helix: 1.60 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.67 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 532 TYR 0.036 0.002 TYR A 590 PHE 0.019 0.001 PHE A 117 TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4178) covalent geometry : angle 0.67418 / 0.32 ( 5676) SS BOND : bond 0.00090 / 0.04 ( 7) SS BOND : angle 0.72040 / 0.56 ( 14) hydrogen bonds : bond 0.04341 / 2.85 ( 259) hydrogen bonds : angle 4.25433 / 3.19 ( 768) link_BETA1-4 : bond 0.00180 / 0.09 ( 1) link_BETA1-4 : angle 0.73065 / 0.53 ( 3) link_NAG-ASN : bond 0.01282 / 0.67 ( 2) link_NAG-ASN : angle 5.95611 / 4.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.146 Fit side-chains REVERT: A 197 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: A 580 ARG cc_start: 0.6696 (ttp-110) cc_final: 0.6120 (ttm-80) outliers start: 15 outliers final: 9 residues processed: 101 average time/residue: 0.0789 time to fit residues: 9.8557 Evaluate side-chains 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.188002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128428 restraints weight = 4928.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133999 restraints weight = 2385.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137579 restraints weight = 1544.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139840 restraints weight = 1191.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140945 restraints weight = 1023.993| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4188 Z= 0.178 Angle : 0.732 12.206 5699 Z= 0.339 Chirality : 0.043 0.265 673 Planarity : 0.004 0.050 698 Dihedral : 3.524 13.501 591 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.92 % Allowed : 21.41 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.35), residues: 554 helix: 1.49 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.62 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 532 TYR 0.033 0.002 TYR A 590 PHE 0.022 0.001 PHE A 117 TRP 0.008 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 4178) covalent geometry : angle 0.70610 / 0.33 ( 5676) SS BOND : bond 0.00134 / 0.07 ( 7) SS BOND : angle 0.75588 / 0.59 ( 14) hydrogen bonds : bond 0.04489 / 2.95 ( 259) hydrogen bonds : angle 4.31849 / 3.24 ( 768) link_BETA1-4 : bond 0.00478 / 0.25 ( 1) link_BETA1-4 : angle 0.73772 / 0.59 ( 3) link_NAG-ASN : bond 0.01281 / 0.67 ( 2) link_NAG-ASN : angle 5.96494 / 4.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8461 (mmt) cc_final: 0.8167 (mmt) REVERT: A 230 PHE cc_start: 0.7069 (m-10) cc_final: 0.6842 (m-10) REVERT: A 580 ARG cc_start: 0.6739 (ttp-110) cc_final: 0.6512 (mtp-110) REVERT: A 614 ARG cc_start: 0.8445 (tpp-160) cc_final: 0.7970 (tpp80) outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 0.0804 time to fit residues: 9.1723 Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 31 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 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 = 0.4190 r_free = 0.4190 target = 0.190275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130602 restraints weight = 4802.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136227 restraints weight = 2332.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139800 restraints weight = 1509.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141567 restraints weight = 1168.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143204 restraints weight = 1018.836| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4188 Z= 0.141 Angle : 0.707 12.186 5699 Z= 0.326 Chirality : 0.042 0.260 673 Planarity : 0.004 0.053 698 Dihedral : 3.519 14.133 591 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.61 % Allowed : 24.02 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.35), residues: 554 helix: 1.74 (0.27), residues: 343 sheet: None (None), residues: 0 loop : -0.51 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 532 TYR 0.034 0.002 TYR A 590 PHE 0.024 0.001 PHE A 117 TRP 0.006 0.001 TRP A 171 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4178) covalent geometry : angle 0.67997 / 0.32 ( 5676) SS BOND : bond 0.00076 / 0.04 ( 7) SS BOND : angle 0.65441 / 0.51 ( 14) hydrogen bonds : bond 0.04272 / 2.83 ( 259) hydrogen bonds : angle 4.23039 / 3.16 ( 768) link_BETA1-4 : bond 0.00166 / 0.09 ( 1) link_BETA1-4 : angle 0.65792 / 0.48 ( 3) link_NAG-ASN : bond 0.01286 / 0.68 ( 2) link_NAG-ASN : angle 5.97668 / 4.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: A 580 ARG cc_start: 0.6699 (ttp-110) cc_final: 0.6074 (ttm-80) REVERT: A 614 ARG cc_start: 0.8479 (tpp-160) cc_final: 0.8076 (tpp80) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.0786 time to fit residues: 8.8372 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 24 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 54 optimal weight: 0.0000 chunk 17 optimal weight: 0.0270 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 178 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 = 0.4207 r_free = 0.4207 target = 0.191705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131862 restraints weight = 4896.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137586 restraints weight = 2374.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141293 restraints weight = 1525.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143630 restraints weight = 1174.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144791 restraints weight = 1005.535| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4188 Z= 0.137 Angle : 0.736 13.766 5699 Z= 0.336 Chirality : 0.042 0.258 673 Planarity : 0.004 0.057 698 Dihedral : 3.460 13.952 591 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.87 % Allowed : 24.54 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.35), residues: 554 helix: 1.80 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.40 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 532 TYR 0.035 0.001 TYR A 590 PHE 0.023 0.001 PHE A 117 TRP 0.006 0.001 TRP A 171 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4178) covalent geometry : angle 0.71046 / 0.33 ( 5676) SS BOND : bond 0.00072 / 0.03 ( 7) SS BOND : angle 0.57707 / 0.44 ( 14) hydrogen bonds : bond 0.04261 / 2.83 ( 259) hydrogen bonds : angle 4.21655 / 3.16 ( 768) link_BETA1-4 : bond 0.00165 / 0.09 ( 1) link_BETA1-4 : angle 0.64645 / 0.48 ( 3) link_NAG-ASN : bond 0.01281 / 0.67 ( 2) link_NAG-ASN : angle 5.98459 / 4.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.157 Fit side-chains REVERT: A 29 MET cc_start: 0.8400 (mmt) cc_final: 0.8194 (mmt) REVERT: A 197 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: A 580 ARG cc_start: 0.6650 (ttp-110) cc_final: 0.6005 (ttm-80) REVERT: A 614 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.8162 (tpp80) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.0811 time to fit residues: 9.1387 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 47 optimal weight: 0.0030 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 178 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 = 0.4199 r_free = 0.4199 target = 0.191010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131278 restraints weight = 4797.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136865 restraints weight = 2342.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140636 restraints weight = 1516.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142525 restraints weight = 1164.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143992 restraints weight = 1011.240| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4188 Z= 0.143 Angle : 0.737 12.179 5699 Z= 0.338 Chirality : 0.043 0.258 673 Planarity : 0.004 0.062 698 Dihedral : 3.469 14.338 591 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.09 % Allowed : 25.33 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.35), residues: 554 helix: 1.80 (0.27), residues: 343 sheet: None (None), residues: 0 loop : -0.39 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 532 TYR 0.035 0.002 TYR A 590 PHE 0.024 0.001 PHE A 117 TRP 0.005 0.001 TRP A 171 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4178) covalent geometry : angle 0.71161 / 0.33 ( 5676) SS BOND : bond 0.00084 / 0.04 ( 7) SS BOND : angle 0.57583 / 0.44 ( 14) hydrogen bonds : bond 0.04219 / 2.78 ( 259) hydrogen bonds : angle 4.19753 / 3.13 ( 768) link_BETA1-4 : bond 0.00231 / 0.12 ( 1) link_BETA1-4 : angle 0.65647 / 0.49 ( 3) link_NAG-ASN : bond 0.01272 / 0.67 ( 2) link_NAG-ASN : angle 5.98204 / 4.03 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.149 Fit side-chains REVERT: A 29 MET cc_start: 0.8412 (mmt) cc_final: 0.8190 (mmt) REVERT: A 57 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8502 (mtp180) REVERT: A 197 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: A 215 ILE cc_start: 0.7231 (tt) cc_final: 0.6959 (tt) REVERT: A 580 ARG cc_start: 0.6647 (ttp-110) cc_final: 0.5967 (ttm-80) REVERT: A 614 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.8156 (tpp80) outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.0823 time to fit residues: 9.0543 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 30.0000 chunk 43 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 178 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 = 0.4193 r_free = 0.4193 target = 0.190235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130478 restraints weight = 4841.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136004 restraints weight = 2358.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139521 restraints weight = 1529.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141382 restraints weight = 1189.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142937 restraints weight = 1032.449| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4188 Z= 0.148 Angle : 0.738 12.171 5699 Z= 0.338 Chirality : 0.043 0.259 673 Planarity : 0.004 0.062 698 Dihedral : 3.464 14.430 591 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.35 % Allowed : 25.33 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.35), residues: 554 helix: 1.78 (0.27), residues: 343 sheet: None (None), residues: 0 loop : -0.39 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 532 TYR 0.034 0.002 TYR A 590 PHE 0.024 0.001 PHE A 117 TRP 0.004 0.001 TRP A 171 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 4178) covalent geometry : angle 0.71244 / 0.33 ( 5676) SS BOND : bond 0.00092 / 0.04 ( 7) SS BOND : angle 0.57267 / 0.44 ( 14) hydrogen bonds : bond 0.04244 / 2.80 ( 259) hydrogen bonds : angle 4.19410 / 3.13 ( 768) link_BETA1-4 : bond 0.00286 / 0.15 ( 1) link_BETA1-4 : angle 0.65266 / 0.50 ( 3) link_NAG-ASN : bond 0.01275 / 0.67 ( 2) link_NAG-ASN : angle 5.97248 / 4.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 928.52 seconds wall clock time: 16 minutes 37.67 seconds (997.67 seconds total)