Starting phenix.real_space_refine on Thu Mar 6 00:00:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnb_34909/03_2025/8hnb_34909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnb_34909/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnb_34909/03_2025/8hnb_34909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnb_34909/03_2025/8hnb_34909.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnb_34909/03_2025/8hnb_34909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnb_34909/03_2025/8hnb_34909.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} 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: 3.02, per 1000 atoms: 0.74 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: 1.03 Conformation dependent library (CDL) restraints added in 483.8 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: 0.45 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: 1.14 Time building geometry restraints manager: 1.27 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: 1.200 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- 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 : 0.007 0.072 4178 Z= 0.446 Angle : 1.349 13.238 5676 Z= 0.919 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (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 TRP 0.019 0.002 TRP A 259 HIS 0.003 0.001 HIS A 575 PHE 0.014 0.001 PHE A 574 TYR 0.025 0.002 TYR A 338 ARG 0.002 0.000 ARG A 246 *********************** 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 : 0.379 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: 0.7135 (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: 0.1830 time to fit residues: 27.7734 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 : 0.394 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4636 r_free = 0.4636 target = 0.236262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.182763 restraints weight = 4433.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.187110 restraints weight = 2588.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189420 restraints weight = 1882.286| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4178 Z= 0.239 Angle : 0.742 10.670 5676 Z= 0.359 Chirality : 0.044 0.326 673 Planarity : 0.004 0.030 698 Dihedral : 7.650 59.628 656 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.87 % Allowed : 16.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.33), residues: 554 helix: 1.23 (0.27), residues: 332 sheet: -5.43 (0.47), residues: 5 loop : -1.18 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 PHE 0.016 0.001 PHE A 73 TYR 0.019 0.002 TYR A 338 ARG 0.008 0.001 ARG A 532 *********************** 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 111 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.1721 time to fit residues: 22.8390 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4545 r_free = 0.4545 target = 0.225059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.170331 restraints weight = 4581.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.174968 restraints weight = 2632.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.177823 restraints weight = 1888.576| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4178 Z= 0.230 Angle : 0.691 9.957 5676 Z= 0.336 Chirality : 0.042 0.285 673 Planarity : 0.004 0.039 698 Dihedral : 5.782 59.563 654 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.22 % Allowed : 18.02 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.35), residues: 554 helix: 1.38 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.72 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 602 HIS 0.016 0.003 HIS A 115 PHE 0.011 0.001 PHE A 73 TYR 0.043 0.002 TYR A 590 ARG 0.008 0.001 ARG A 532 *********************** 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 114 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.466 Fit side-chains REVERT: A 27 LEU cc_start: 0.7306 (tt) cc_final: 0.6875 (tt) REVERT: A 48 MET cc_start: 0.8811 (tpt) cc_final: 0.8570 (tpt) REVERT: A 580 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6838 (ttm-80) REVERT: A 582 LEU cc_start: 0.8761 (mt) cc_final: 0.8546 (mp) outliers start: 20 outliers final: 10 residues processed: 104 average time/residue: 0.1798 time to fit residues: 22.9143 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE 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 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 589 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.0060 chunk 27 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4193 r_free = 0.4193 target = 0.191472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.132510 restraints weight = 4814.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138060 restraints weight = 2399.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141626 restraints weight = 1566.524| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4178 Z= 0.204 Angle : 0.667 9.892 5676 Z= 0.323 Chirality : 0.042 0.269 673 Planarity : 0.004 0.038 698 Dihedral : 5.467 54.118 654 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.35), residues: 554 helix: 1.59 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.007 0.002 HIS A 115 PHE 0.012 0.001 PHE A 73 TYR 0.044 0.002 TYR A 590 ARG 0.009 0.001 ARG A 532 *********************** 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 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.459 Fit side-chains REVERT: A 27 LEU cc_start: 0.6521 (tt) cc_final: 0.6109 (tt) REVERT: A 117 PHE cc_start: 0.8296 (m-10) cc_final: 0.7965 (m-10) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.2051 time to fit residues: 24.7395 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 40.0000 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4180 r_free = 0.4180 target = 0.189452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130141 restraints weight = 4928.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135719 restraints weight = 2369.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139372 restraints weight = 1527.619| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4178 Z= 0.221 Angle : 0.683 9.836 5676 Z= 0.325 Chirality : 0.041 0.254 673 Planarity : 0.004 0.040 698 Dihedral : 5.340 53.380 654 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.66 % Allowed : 20.10 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.35), residues: 554 helix: 1.67 (0.27), residues: 341 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 115 PHE 0.013 0.001 PHE A 73 TYR 0.038 0.002 TYR A 590 ARG 0.009 0.001 ARG A 532 *********************** 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 104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.879 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.2736 time to fit residues: 33.8153 Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127011 restraints weight = 4878.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132451 restraints weight = 2404.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135988 restraints weight = 1571.332| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4178 Z= 0.267 Angle : 0.684 9.804 5676 Z= 0.329 Chirality : 0.042 0.256 673 Planarity : 0.004 0.046 698 Dihedral : 5.298 53.086 654 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.39 % Allowed : 21.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 554 helix: 1.46 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.63 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 115 PHE 0.024 0.001 PHE A 117 TYR 0.037 0.002 TYR A 590 ARG 0.010 0.001 ARG A 532 *********************** 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 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.952 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.3546 time to fit residues: 41.3350 Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 30.0000 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 10 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4170 r_free = 0.4170 target = 0.187967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129347 restraints weight = 4913.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134707 restraints weight = 2444.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138140 restraints weight = 1613.168| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4178 Z= 0.225 Angle : 0.684 9.797 5676 Z= 0.326 Chirality : 0.041 0.250 673 Planarity : 0.004 0.052 698 Dihedral : 5.311 53.288 654 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.92 % Allowed : 22.45 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.35), residues: 554 helix: 1.64 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.59 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 PHE 0.026 0.001 PHE A 117 TYR 0.035 0.002 TYR A 590 ARG 0.012 0.002 ARG A 532 *********************** 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 : 0.839 Fit side-chains REVERT: A 29 MET cc_start: 0.8430 (mmt) cc_final: 0.8159 (mmt) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.2306 time to fit residues: 27.1165 Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 172 ILE 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 589 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 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 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 = 0.4183 r_free = 0.4183 target = 0.188891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129129 restraints weight = 4790.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134657 restraints weight = 2360.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138225 restraints weight = 1544.933| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4178 Z= 0.221 Angle : 0.689 9.789 5676 Z= 0.325 Chirality : 0.041 0.249 673 Planarity : 0.004 0.056 698 Dihedral : 5.295 53.414 654 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.13 % Allowed : 23.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.35), residues: 554 helix: 1.55 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.48 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.004 0.001 HIS A 115 PHE 0.028 0.001 PHE A 117 TYR 0.035 0.002 TYR A 590 ARG 0.012 0.002 ARG A 532 *********************** 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 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.432 Fit side-chains REVERT: A 197 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7674 (m-30) outliers start: 12 outliers final: 11 residues processed: 90 average time/residue: 0.2112 time to fit residues: 23.2289 Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 172 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4178 r_free = 0.4178 target = 0.188452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129082 restraints weight = 4793.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134547 restraints weight = 2357.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138138 restraints weight = 1539.375| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4178 Z= 0.217 Angle : 0.688 9.784 5676 Z= 0.323 Chirality : 0.041 0.249 673 Planarity : 0.004 0.056 698 Dihedral : 5.288 53.465 654 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.39 % Allowed : 23.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.35), residues: 554 helix: 1.60 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.50 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 575 PHE 0.027 0.001 PHE A 117 TYR 0.035 0.002 TYR A 590 ARG 0.013 0.002 ARG A 532 *********************** 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 : 0.492 Fit side-chains REVERT: A 29 MET cc_start: 0.8433 (mmt) cc_final: 0.8210 (mmt) REVERT: A 57 ARG cc_start: 0.8949 (mtm180) cc_final: 0.8687 (mtm180) REVERT: A 170 MET cc_start: 0.8455 (mmm) cc_final: 0.8181 (mmp) REVERT: A 197 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: A 246 ARG cc_start: 0.8949 (mmp80) cc_final: 0.8723 (mmp80) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.2537 time to fit residues: 28.3785 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 172 ILE 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 46 optimal weight: 0.0270 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4188 r_free = 0.4188 target = 0.189475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129515 restraints weight = 4859.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135136 restraints weight = 2372.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138600 restraints weight = 1545.025| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4178 Z= 0.225 Angle : 0.702 9.783 5676 Z= 0.334 Chirality : 0.041 0.249 673 Planarity : 0.004 0.060 698 Dihedral : 5.300 53.457 654 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.13 % Allowed : 24.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.35), residues: 554 helix: 1.63 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.50 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.005 0.001 HIS A 115 PHE 0.025 0.001 PHE A 117 TYR 0.035 0.001 TYR A 590 ARG 0.015 0.001 ARG A 532 ********************** 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 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: A 251 ASP cc_start: 0.8075 (t0) cc_final: 0.7844 (t0) outliers start: 12 outliers final: 10 residues processed: 95 average time/residue: 0.1849 time to fit residues: 21.2946 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 : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 172 ILE 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 31 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 0.0040 chunk 35 optimal weight: 0.0040 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4197 r_free = 0.4197 target = 0.190677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131806 restraints weight = 4819.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137381 restraints weight = 2341.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141025 restraints weight = 1513.925| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4178 Z= 0.211 Angle : 0.727 11.345 5676 Z= 0.338 Chirality : 0.041 0.247 673 Planarity : 0.004 0.060 698 Dihedral : 5.302 53.596 654 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.09 % Allowed : 25.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.35), residues: 554 helix: 1.75 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.38 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.005 0.002 HIS A 115 PHE 0.023 0.001 PHE A 117 TYR 0.036 0.001 TYR A 590 ARG 0.014 0.002 ARG A 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.14 seconds wall clock time: 37 minutes 35.34 seconds (2255.34 seconds total)