Starting phenix.real_space_refine on Fri Aug 22 14:28:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnb_34909/08_2025/8hnb_34909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnb_34909/08_2025/8hnb_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_34909/08_2025/8hnb_34909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnb_34909/08_2025/8hnb_34909.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnb_34909/08_2025/8hnb_34909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnb_34909/08_2025/8hnb_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.38, per 1000 atoms: 0.34 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: 0.39 Conformation dependent library (CDL) restraints added in 175.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.15 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: 0.61 Time building geometry restraints manager: 0.52 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 - 21.06: 2303 21.06 - 42.12: 133 42.12 - 63.18: 16 63.18 - 84.24: 2 84.24 - 105.30: 8 Dihedral angle restraints: 2462 sinusoidal: 861 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 2459 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.210 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 14.650 105.302 1421 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 aren 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 covalent geometry : bond 0.00702 ( 4178) covalent geometry : angle 1.34865 ( 5676) SS BOND : bond 0.00758 ( 7) SS BOND : angle 1.49258 ( 14) hydrogen bonds : bond 0.22210 ( 259) hydrogen bonds : angle 8.19178 ( 768) link_BETA1-4 : bond 0.04861 ( 1) link_BETA1-4 : angle 9.14291 ( 3) link_NAG-ASN : bond 0.15224 ( 2) link_NAG-ASN : angle 8.27917 ( 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 : 0.157 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: 0.0838 time to fit residues: 12.6844 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 : 0.159 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4632 r_free = 0.4632 target = 0.235835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.182129 restraints weight = 4484.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186630 restraints weight = 2608.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.188960 restraints weight = 1886.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.190838 restraints weight = 1577.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.191304 restraints weight = 1419.798| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2839 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= 0.176 Angle : 0.760 12.839 5699 Z= 0.362 Chirality : 0.043 0.319 673 Planarity : 0.004 0.029 698 Dihedral : 7.784 57.482 656 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.61 % Allowed : 17.23 % Favored : 80.16 % 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: 0.41 (0.33), residues: 554 helix: 1.29 (0.27), residues: 332 sheet: -5.40 (0.50), residues: 5 loop : -1.19 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 532 TYR 0.019 0.002 TYR A 338 PHE 0.014 0.001 PHE A 73 TRP 0.012 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4178) covalent geometry : angle 0.72692 ( 5676) SS BOND : bond 0.00288 ( 7) SS BOND : angle 0.91750 ( 14) hydrogen bonds : bond 0.06024 ( 259) hydrogen bonds : angle 5.16180 ( 768) link_BETA1-4 : bond 0.01407 ( 1) link_BETA1-4 : angle 3.37304 ( 3) link_NAG-ASN : bond 0.01275 ( 2) link_NAG-ASN : angle 6.35654 ( 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 : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8856 (tpt) cc_final: 0.8584 (tpt) REVERT: A 56 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7691 (tm-30) outliers start: 10 outliers final: 8 residues processed: 105 average time/residue: 0.0820 time to fit residues: 10.5042 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 186 THR 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: 0.0020 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4599 r_free = 0.4599 target = 0.231917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178105 restraints weight = 4520.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.182610 restraints weight = 2623.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.185302 restraints weight = 1897.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.186599 restraints weight = 1575.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.187191 restraints weight = 1425.776| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4188 Z= 0.152 Angle : 0.720 12.295 5699 Z= 0.341 Chirality : 0.041 0.289 673 Planarity : 0.004 0.031 698 Dihedral : 6.005 59.456 654 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.92 % Allowed : 19.58 % 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 aren not related in a simple way. whole: 0.88 (0.35), residues: 554 helix: 1.51 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 532 TYR 0.036 0.002 TYR A 590 PHE 0.013 0.001 PHE A 73 TRP 0.008 0.001 TRP A 171 HIS 0.015 0.003 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4178) covalent geometry : angle 0.69317 ( 5676) SS BOND : bond 0.00545 ( 7) SS BOND : angle 0.82940 ( 14) hydrogen bonds : bond 0.05204 ( 259) hydrogen bonds : angle 4.82117 ( 768) link_BETA1-4 : bond 0.00588 ( 1) link_BETA1-4 : angle 1.11703 ( 3) link_NAG-ASN : bond 0.01558 ( 2) link_NAG-ASN : angle 5.93598 ( 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 106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.097 Fit side-chains REVERT: A 27 LEU cc_start: 0.7212 (tt) cc_final: 0.6802 (tt) REVERT: A 48 MET cc_start: 0.8791 (tpt) cc_final: 0.8438 (tpt) REVERT: A 57 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8435 (mtp180) REVERT: A 176 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7178 (tpp) REVERT: A 580 ARG cc_start: 0.7196 (ttp-110) cc_final: 0.6836 (ttm-80) outliers start: 15 outliers final: 8 residues processed: 99 average time/residue: 0.0778 time to fit residues: 9.4443 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 176 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.190416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130715 restraints weight = 4828.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136088 restraints weight = 2475.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139672 restraints weight = 1636.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141870 restraints weight = 1271.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142858 restraints weight = 1094.478| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4188 Z= 0.154 Angle : 0.685 12.224 5699 Z= 0.323 Chirality : 0.041 0.274 673 Planarity : 0.004 0.038 698 Dihedral : 5.503 55.237 654 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.44 % Allowed : 20.10 % Favored : 75.46 % 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: 1.06 (0.35), residues: 554 helix: 1.57 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 532 TYR 0.020 0.002 TYR A 590 PHE 0.012 0.001 PHE A 73 TRP 0.013 0.001 TRP A 470 HIS 0.016 0.003 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4178) covalent geometry : angle 0.65616 ( 5676) SS BOND : bond 0.00418 ( 7) SS BOND : angle 1.05141 ( 14) hydrogen bonds : bond 0.04833 ( 259) hydrogen bonds : angle 4.55015 ( 768) link_BETA1-4 : bond 0.00394 ( 1) link_BETA1-4 : angle 0.96728 ( 3) link_NAG-ASN : bond 0.01389 ( 2) link_NAG-ASN : angle 5.95906 ( 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 105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.182 Fit side-chains REVERT: A 27 LEU cc_start: 0.6667 (tt) cc_final: 0.6271 (tt) REVERT: A 57 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8394 (mtp180) REVERT: A 369 GLN cc_start: 0.7379 (mp10) cc_final: 0.6774 (mp10) REVERT: A 580 ARG cc_start: 0.6940 (ttp-110) cc_final: 0.6727 (mtp-110) REVERT: A 582 LEU cc_start: 0.8839 (mt) cc_final: 0.8585 (mp) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.0880 time to fit residues: 10.6017 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 : 0.152 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 0.0170 chunk 43 optimal weight: 30.0000 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 40.0000 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4150 r_free = 0.4150 target = 0.186535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127131 restraints weight = 4820.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132527 restraints weight = 2370.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135942 restraints weight = 1543.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137935 restraints weight = 1202.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139050 restraints weight = 1040.575| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4188 Z= 0.188 Angle : 0.717 12.242 5699 Z= 0.338 Chirality : 0.043 0.259 673 Planarity : 0.004 0.042 698 Dihedral : 5.343 53.284 654 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.74 % Allowed : 18.80 % Favored : 75.46 % 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: 0.86 (0.34), residues: 554 helix: 1.38 (0.27), residues: 343 sheet: None (None), residues: 0 loop : -0.74 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 532 TYR 0.023 0.002 TYR A 590 PHE 0.012 0.001 PHE A 73 TRP 0.010 0.001 TRP A 470 HIS 0.011 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4178) covalent geometry : angle 0.68993 ( 5676) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.96238 ( 14) hydrogen bonds : bond 0.04962 ( 259) hydrogen bonds : angle 4.57088 ( 768) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 0.97987 ( 3) link_NAG-ASN : bond 0.01270 ( 2) link_NAG-ASN : angle 6.00055 ( 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: 22 poor density : 83 time to evaluate : 0.156 Fit side-chains REVERT: A 57 ARG cc_start: 0.8675 (mtm-85) cc_final: 0.8303 (mtp180) REVERT: A 580 ARG cc_start: 0.6782 (ttp-110) cc_final: 0.6237 (ttm-80) REVERT: A 582 LEU cc_start: 0.8749 (mt) cc_final: 0.8541 (mp) outliers start: 22 outliers final: 14 residues processed: 95 average time/residue: 0.0768 time to fit residues: 8.8286 Evaluate side-chains 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4192 r_free = 0.4192 target = 0.190735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131186 restraints weight = 4837.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136842 restraints weight = 2340.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140508 restraints weight = 1515.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142602 restraints weight = 1166.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143709 restraints weight = 1004.090| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4188 Z= 0.139 Angle : 0.686 12.269 5699 Z= 0.319 Chirality : 0.041 0.251 673 Planarity : 0.004 0.042 698 Dihedral : 5.290 53.267 654 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.66 % Allowed : 20.63 % 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 aren not related in a simple way. whole: 1.16 (0.35), residues: 554 helix: 1.63 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 532 TYR 0.022 0.001 TYR A 590 PHE 0.014 0.001 PHE A 73 TRP 0.008 0.001 TRP A 254 HIS 0.005 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4178) covalent geometry : angle 0.65696 ( 5676) SS BOND : bond 0.00090 ( 7) SS BOND : angle 0.72412 ( 14) hydrogen bonds : bond 0.04427 ( 259) hydrogen bonds : angle 4.35046 ( 768) link_BETA1-4 : bond 0.00343 ( 1) link_BETA1-4 : angle 0.98024 ( 3) link_NAG-ASN : bond 0.01273 ( 2) link_NAG-ASN : angle 6.04255 ( 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 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.147 Fit side-chains REVERT: A 57 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8359 (mtp180) REVERT: A 176 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6672 (mmm) REVERT: A 197 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: A 580 ARG cc_start: 0.6716 (ttp-110) cc_final: 0.6137 (ttm-80) REVERT: A 614 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7524 (tpp80) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.0895 time to fit residues: 10.0357 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 SER 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 579 ILE 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: 8.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4170 r_free = 0.4170 target = 0.188676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129683 restraints weight = 4936.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135254 restraints weight = 2382.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138874 restraints weight = 1543.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141140 restraints weight = 1185.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142222 restraints weight = 1012.727| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4188 Z= 0.148 Angle : 0.716 12.302 5699 Z= 0.329 Chirality : 0.042 0.249 673 Planarity : 0.004 0.051 698 Dihedral : 5.246 53.204 654 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.39 % Allowed : 22.72 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.35), residues: 554 helix: 1.61 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 532 TYR 0.022 0.001 TYR A 590 PHE 0.010 0.001 PHE A 73 TRP 0.005 0.001 TRP A 254 HIS 0.005 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4178) covalent geometry : angle 0.68831 ( 5676) SS BOND : bond 0.00097 ( 7) SS BOND : angle 0.68675 ( 14) hydrogen bonds : bond 0.04332 ( 259) hydrogen bonds : angle 4.27238 ( 768) link_BETA1-4 : bond 0.00408 ( 1) link_BETA1-4 : angle 1.01282 ( 3) link_NAG-ASN : bond 0.01261 ( 2) link_NAG-ASN : angle 6.04845 ( 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: 13 poor density : 85 time to evaluate : 0.154 Fit side-chains REVERT: A 29 MET cc_start: 0.8444 (mmt) cc_final: 0.8167 (mmt) REVERT: A 57 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8293 (mtp180) REVERT: A 176 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6763 (mmm) REVERT: A 197 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: A 580 ARG cc_start: 0.6731 (ttp-110) cc_final: 0.6152 (ttm-80) REVERT: A 614 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7636 (tpp80) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.0851 time to fit residues: 9.6305 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 SER 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 579 ILE 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: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 40.0000 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4171 r_free = 0.4171 target = 0.188577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129856 restraints weight = 4846.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135356 restraints weight = 2358.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138920 restraints weight = 1527.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140980 restraints weight = 1177.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142452 restraints weight = 1013.672| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 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 0.045 4188 Z= 0.145 Angle : 0.708 12.309 5699 Z= 0.325 Chirality : 0.041 0.249 673 Planarity : 0.004 0.054 698 Dihedral : 5.220 53.288 654 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.66 % Allowed : 22.45 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.35), residues: 554 helix: 1.67 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.58 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 532 TYR 0.022 0.001 TYR A 590 PHE 0.008 0.001 PHE A 175 TRP 0.004 0.001 TRP A 259 HIS 0.006 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4178) covalent geometry : angle 0.68082 ( 5676) SS BOND : bond 0.00099 ( 7) SS BOND : angle 0.67421 ( 14) hydrogen bonds : bond 0.04273 ( 259) hydrogen bonds : angle 4.20212 ( 768) link_BETA1-4 : bond 0.00372 ( 1) link_BETA1-4 : angle 0.98274 ( 3) link_NAG-ASN : bond 0.01262 ( 2) link_NAG-ASN : angle 6.05081 ( 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 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.149 Fit side-chains REVERT: A 57 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8302 (mtp180) REVERT: A 118 MET cc_start: 0.8191 (mmm) cc_final: 0.7943 (mpp) REVERT: A 176 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6752 (mmm) REVERT: A 197 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: A 580 ARG cc_start: 0.6723 (ttp-110) cc_final: 0.6081 (ttm-80) REVERT: A 614 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7788 (tpp80) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.0802 time to fit residues: 9.2793 Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 SER 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 579 ILE 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: 0.8980 chunk 52 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4170 r_free = 0.4170 target = 0.188584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130554 restraints weight = 4905.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135972 restraints weight = 2421.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139242 restraints weight = 1574.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141597 restraints weight = 1227.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142817 restraints weight = 1049.665| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4711 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 : 0.708 12.306 5699 Z= 0.323 Chirality : 0.041 0.248 673 Planarity : 0.004 0.057 698 Dihedral : 5.213 53.329 654 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.39 % Allowed : 22.72 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.35), residues: 554 helix: 1.69 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.55 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 532 TYR 0.023 0.001 TYR A 590 PHE 0.008 0.001 PHE A 175 TRP 0.004 0.001 TRP A 259 HIS 0.006 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4178) covalent geometry : angle 0.68087 ( 5676) SS BOND : bond 0.00094 ( 7) SS BOND : angle 0.63471 ( 14) hydrogen bonds : bond 0.04242 ( 259) hydrogen bonds : angle 4.16658 ( 768) link_BETA1-4 : bond 0.00382 ( 1) link_BETA1-4 : angle 0.96553 ( 3) link_NAG-ASN : bond 0.01266 ( 2) link_NAG-ASN : angle 6.05430 ( 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 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.130 Fit side-chains REVERT: A 57 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8302 (mtp180) REVERT: A 118 MET cc_start: 0.8171 (mmm) cc_final: 0.7958 (mpp) REVERT: A 176 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6804 (mmm) REVERT: A 197 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: A 254 TRP cc_start: 0.7850 (t-100) cc_final: 0.6765 (t-100) REVERT: A 580 ARG cc_start: 0.6720 (ttp-110) cc_final: 0.6059 (ttm-80) REVERT: A 614 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7869 (tpp80) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.0771 time to fit residues: 8.7463 Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP 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 579 ILE 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: 0.8980 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 0.0030 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4177 r_free = 0.4177 target = 0.189447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130746 restraints weight = 4775.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136349 restraints weight = 2308.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139962 restraints weight = 1490.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142002 restraints weight = 1148.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143031 restraints weight = 990.539| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4188 Z= 0.143 Angle : 0.723 12.300 5699 Z= 0.332 Chirality : 0.042 0.248 673 Planarity : 0.004 0.061 698 Dihedral : 5.244 53.372 654 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.66 % Allowed : 22.45 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.35), residues: 554 helix: 1.72 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.42 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 532 TYR 0.023 0.001 TYR A 590 PHE 0.008 0.001 PHE A 175 TRP 0.005 0.001 TRP A 171 HIS 0.005 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4178) covalent geometry : angle 0.69634 ( 5676) SS BOND : bond 0.00082 ( 7) SS BOND : angle 0.59026 ( 14) hydrogen bonds : bond 0.04210 ( 259) hydrogen bonds : angle 4.19759 ( 768) link_BETA1-4 : bond 0.00494 ( 1) link_BETA1-4 : angle 0.98221 ( 3) link_NAG-ASN : bond 0.01264 ( 2) link_NAG-ASN : angle 6.05573 ( 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 98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8271 (mtp180) REVERT: A 176 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6806 (mmm) REVERT: A 197 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: A 246 ARG cc_start: 0.8924 (mmp80) cc_final: 0.8710 (mmp80) REVERT: A 254 TRP cc_start: 0.7813 (t-100) cc_final: 0.6746 (t-100) REVERT: A 424 LEU cc_start: 0.8621 (tp) cc_final: 0.8388 (tp) REVERT: A 580 ARG cc_start: 0.6719 (ttp-110) cc_final: 0.6512 (mtp-110) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.0759 time to fit residues: 8.5784 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP 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 579 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 50.0000 chunk 43 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4168 r_free = 0.4168 target = 0.188406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129695 restraints weight = 4836.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135237 restraints weight = 2344.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138856 restraints weight = 1513.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140564 restraints weight = 1165.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142254 restraints weight = 1017.514| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4942 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= 0.146 Angle : 0.733 12.302 5699 Z= 0.337 Chirality : 0.042 0.249 673 Planarity : 0.004 0.061 698 Dihedral : 5.222 53.386 654 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.39 % Allowed : 24.28 % 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 aren not related in a simple way. whole: 1.40 (0.35), residues: 554 helix: 1.70 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -0.39 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 532 TYR 0.024 0.001 TYR A 590 PHE 0.024 0.001 PHE A 391 TRP 0.006 0.001 TRP A 258 HIS 0.007 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4178) covalent geometry : angle 0.70682 ( 5676) SS BOND : bond 0.00084 ( 7) SS BOND : angle 0.59268 ( 14) hydrogen bonds : bond 0.04218 ( 259) hydrogen bonds : angle 4.15650 ( 768) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 0.92839 ( 3) link_NAG-ASN : bond 0.01264 ( 2) link_NAG-ASN : angle 6.05772 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1002.01 seconds wall clock time: 17 minutes 53.18 seconds (1073.18 seconds total)