Starting phenix.real_space_refine on Fri Aug 22 15:04:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ym0_39393/08_2025/8ym0_39393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ym0_39393/08_2025/8ym0_39393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ym0_39393/08_2025/8ym0_39393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ym0_39393/08_2025/8ym0_39393.map" model { file = "/net/cci-nas-00/data/ceres_data/8ym0_39393/08_2025/8ym0_39393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ym0_39393/08_2025/8ym0_39393.cif" } resolution = 3.05 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= 0.049 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 41 5.16 5 C 2963 2.51 5 N 783 2.21 5 O 893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 4680 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4630 Classifications: {'peptide': 582} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 557} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 50 Unusual residues: {'OCA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.59, per 1000 atoms: 0.34 Number of scatterers: 4680 At special positions: 0 Unit cell: (69.72, 93.24, 99.12, 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 41 16.00 O 893 8.00 N 783 7.00 C 2963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 438 " distance=2.04 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 182.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 75.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 56 removed outlier: 3.513A pdb=" N HIS A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 79 removed outlier: 4.383A pdb=" N VAL A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.650A pdb=" N ALA A 92 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.787A pdb=" N TYR A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.946A pdb=" N PHE A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 202 removed outlier: 3.912A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.627A pdb=" N GLU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 223 removed outlier: 3.821A pdb=" N PHE A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 247 removed outlier: 3.546A pdb=" N GLU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 246 " --> pdb=" O HIS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 3.518A pdb=" N ALA A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.976A pdb=" N LYS A 281 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 4.018A pdb=" N SER A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.740A pdb=" N ASP A 308 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.949A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.650A pdb=" N LYS A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 376 through 396 removed outlier: 4.429A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.501A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 415 removed outlier: 4.243A pdb=" N LYS A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 441 through 466 removed outlier: 4.400A pdb=" N MET A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 3.903A pdb=" N ASP A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.511A pdb=" N THR A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.504A pdb=" N THR A 506 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 507 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 508 " --> pdb=" O GLU A 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 508' Processing helix chain 'A' and resid 517 through 536 removed outlier: 3.709A pdb=" N ARG A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.805A pdb=" N ASP A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 558 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 582 removed outlier: 4.097A pdb=" N ALA A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) 261 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: 0.66 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1544 1.35 - 1.46: 1001 1.46 - 1.58: 2173 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4765 Sorted by residual: bond pdb=" C2 OCA A 605 " pdb=" C3 OCA A 605 " ideal model delta sigma weight residual 1.520 1.486 0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C4 OCA A 605 " pdb=" C5 OCA A 605 " ideal model delta sigma weight residual 1.524 1.496 0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" N LYS A 536 " pdb=" CA LYS A 536 " ideal model delta sigma weight residual 1.463 1.477 -0.015 1.11e-02 8.12e+03 1.76e+00 bond pdb=" C5 OCA A 605 " pdb=" C6 OCA A 605 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C2 OCA A 604 " pdb=" C3 OCA A 604 " ideal model delta sigma weight residual 1.520 1.495 0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 4760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 6158 1.07 - 2.14: 188 2.14 - 3.21: 44 3.21 - 4.28: 13 4.28 - 5.34: 8 Bond angle restraints: 6411 Sorted by residual: angle pdb=" CA LYS A 536 " pdb=" C LYS A 536 " pdb=" N PRO A 537 " ideal model delta sigma weight residual 117.59 120.79 -3.20 1.03e+00 9.43e-01 9.67e+00 angle pdb=" C HIS A 535 " pdb=" N LYS A 536 " pdb=" CA LYS A 536 " ideal model delta sigma weight residual 123.15 119.56 3.59 1.21e+00 6.83e-01 8.81e+00 angle pdb=" CA LYS A 536 " pdb=" C LYS A 536 " pdb=" O LYS A 536 " ideal model delta sigma weight residual 121.02 117.75 3.27 1.28e+00 6.10e-01 6.51e+00 angle pdb=" N LYS A 536 " pdb=" CA LYS A 536 " pdb=" CB LYS A 536 " ideal model delta sigma weight residual 110.99 106.99 4.00 1.58e+00 4.01e-01 6.42e+00 angle pdb=" CA VAL A 310 " pdb=" C VAL A 310 " pdb=" N GLU A 311 " ideal model delta sigma weight residual 116.60 120.16 -3.56 1.45e+00 4.76e-01 6.04e+00 ... (remaining 6406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2609 17.83 - 35.67: 316 35.67 - 53.50: 58 53.50 - 71.34: 18 71.34 - 89.17: 11 Dihedral angle restraints: 3012 sinusoidal: 1273 harmonic: 1739 Sorted by residual: dihedral pdb=" CB CYS A 360 " pdb=" SG CYS A 360 " pdb=" SG CYS A 369 " pdb=" CB CYS A 369 " ideal model delta sinusoidal sigma weight residual -86.00 -168.20 82.20 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual 93.00 170.78 -77.78 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual -86.00 -161.54 75.54 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 3009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 464 0.031 - 0.062: 184 0.062 - 0.094: 40 0.094 - 0.125: 17 0.125 - 0.156: 2 Chirality restraints: 707 Sorted by residual: chirality pdb=" CA LYS A 536 " pdb=" N LYS A 536 " pdb=" C LYS A 536 " pdb=" CB LYS A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA LYS A 225 " pdb=" N LYS A 225 " pdb=" C LYS A 225 " pdb=" CB LYS A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA CYS A 169 " pdb=" N CYS A 169 " pdb=" C CYS A 169 " pdb=" CB CYS A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 704 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 179 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 180 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 281 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 282 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 497 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.33e+00 pdb=" C TYR A 497 " 0.020 2.00e-02 2.50e+03 pdb=" O TYR A 497 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL A 498 " -0.007 2.00e-02 2.50e+03 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 670 2.75 - 3.29: 4395 3.29 - 3.83: 7520 3.83 - 4.36: 8847 4.36 - 4.90: 15231 Nonbonded interactions: 36663 Sorted by model distance: nonbonded pdb=" O ASP A 72 " pdb=" OG1 THR A 76 " model vdw 2.217 3.040 nonbonded pdb=" O CYS A 34 " pdb=" OH TYR A 140 " model vdw 2.245 3.040 nonbonded pdb=" O LEU A 516 " pdb=" NH2 ARG A 521 " model vdw 2.300 3.120 nonbonded pdb=" O GLU A 505 " pdb=" OG1 THR A 508 " model vdw 2.318 3.040 nonbonded pdb=" OE2 GLU A 153 " pdb=" ND1 HIS A 288 " model vdw 2.334 3.120 ... (remaining 36658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 6.110 Find NCS groups from input model: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4782 Z= 0.134 Angle : 0.508 5.345 6445 Z= 0.267 Chirality : 0.037 0.156 707 Planarity : 0.004 0.047 834 Dihedral : 16.266 89.170 1821 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.56 (0.35), residues: 580 helix: 0.21 (0.27), residues: 394 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 98 TYR 0.018 0.001 TYR A 150 PHE 0.004 0.001 PHE A 149 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4765) covalent geometry : angle 0.50120 ( 6411) SS BOND : bond 0.00199 ( 17) SS BOND : angle 1.20989 ( 34) hydrogen bonds : bond 0.23967 ( 261) hydrogen bonds : angle 6.03230 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0873 time to fit residues: 5.9845 Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 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 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.183648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124151 restraints weight = 4698.645| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.55 r_work: 0.3035 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4782 Z= 0.122 Angle : 0.504 5.277 6445 Z= 0.263 Chirality : 0.037 0.120 707 Planarity : 0.004 0.042 834 Dihedral : 7.820 73.828 653 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.39 % Allowed : 6.68 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.14 (0.36), residues: 580 helix: 0.88 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.70 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.019 0.001 TYR A 150 PHE 0.010 0.001 PHE A 49 TRP 0.002 0.001 TRP A 214 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4765) covalent geometry : angle 0.50061 ( 6411) SS BOND : bond 0.00270 ( 17) SS BOND : angle 0.90954 ( 34) hydrogen bonds : bond 0.04408 ( 261) hydrogen bonds : angle 3.68272 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.131 Fit side-chains REVERT: A 45 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 104 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7446 (mm-40) REVERT: A 351 LYS cc_start: 0.7520 (mtpt) cc_final: 0.7130 (ttpt) REVERT: A 466 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7373 (mmtt) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.0859 time to fit residues: 5.4203 Evaluate side-chains 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.181266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122356 restraints weight = 4748.327| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.33 r_work: 0.2995 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4782 Z= 0.133 Angle : 0.496 5.765 6445 Z= 0.255 Chirality : 0.038 0.131 707 Planarity : 0.004 0.042 834 Dihedral : 7.336 79.098 653 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.98 % Allowed : 10.02 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.42 (0.36), residues: 580 helix: 1.12 (0.27), residues: 405 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.015 0.001 TYR A 150 PHE 0.008 0.001 PHE A 149 TRP 0.003 0.001 TRP A 214 HIS 0.011 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4765) covalent geometry : angle 0.49327 ( 6411) SS BOND : bond 0.00280 ( 17) SS BOND : angle 0.89711 ( 34) hydrogen bonds : bond 0.04402 ( 261) hydrogen bonds : angle 3.49238 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.184 Fit side-chains REVERT: A 45 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 87 MET cc_start: 0.5655 (mmm) cc_final: 0.5424 (mmm) REVERT: A 104 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7453 (mm-40) REVERT: A 466 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7212 (mmtt) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.0839 time to fit residues: 5.1880 Evaluate side-chains 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.178937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111753 restraints weight = 4710.841| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.27 r_work: 0.3080 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4782 Z= 0.168 Angle : 0.528 5.967 6445 Z= 0.270 Chirality : 0.039 0.153 707 Planarity : 0.004 0.042 834 Dihedral : 7.403 82.604 653 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.38 % Allowed : 12.18 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.40 (0.36), residues: 580 helix: 1.10 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.70 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 98 TYR 0.013 0.002 TYR A 370 PHE 0.016 0.001 PHE A 49 TRP 0.003 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 4765) covalent geometry : angle 0.52355 ( 6411) SS BOND : bond 0.00334 ( 17) SS BOND : angle 1.03135 ( 34) hydrogen bonds : bond 0.04696 ( 261) hydrogen bonds : angle 3.51201 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.198 Fit side-chains REVERT: A 87 MET cc_start: 0.5826 (mmm) cc_final: 0.5509 (mmm) REVERT: A 104 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7420 (mm-40) REVERT: A 466 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7363 (mmtt) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.0722 time to fit residues: 4.6953 Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.181430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115154 restraints weight = 4742.028| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.27 r_work: 0.3040 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4782 Z= 0.108 Angle : 0.478 6.033 6445 Z= 0.246 Chirality : 0.037 0.135 707 Planarity : 0.004 0.041 834 Dihedral : 6.903 82.425 653 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.79 % Allowed : 14.15 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.59 (0.36), residues: 580 helix: 1.30 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.79 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.009 0.001 TYR A 161 PHE 0.007 0.001 PHE A 19 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4765) covalent geometry : angle 0.47402 ( 6411) SS BOND : bond 0.00270 ( 17) SS BOND : angle 0.93841 ( 34) hydrogen bonds : bond 0.03718 ( 261) hydrogen bonds : angle 3.38806 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7883 (mt-10) REVERT: A 104 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7341 (mm-40) REVERT: A 466 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7254 (mmtt) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.0619 time to fit residues: 3.9452 Evaluate side-chains 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 523 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.180224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112759 restraints weight = 4787.534| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.30 r_work: 0.2937 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4782 Z= 0.139 Angle : 0.503 6.131 6445 Z= 0.258 Chirality : 0.038 0.137 707 Planarity : 0.004 0.041 834 Dihedral : 7.017 83.355 653 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.18 % Allowed : 14.54 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.58 (0.36), residues: 580 helix: 1.29 (0.27), residues: 403 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.012 0.001 TYR A 370 PHE 0.017 0.001 PHE A 49 TRP 0.003 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4765) covalent geometry : angle 0.49911 ( 6411) SS BOND : bond 0.00307 ( 17) SS BOND : angle 1.03267 ( 34) hydrogen bonds : bond 0.04250 ( 261) hydrogen bonds : angle 3.41420 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7331 (mm-40) REVERT: A 466 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7239 (mmtt) outliers start: 6 outliers final: 6 residues processed: 47 average time/residue: 0.0659 time to fit residues: 4.2239 Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 523 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.182603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116077 restraints weight = 4702.328| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.27 r_work: 0.3047 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4782 Z= 0.103 Angle : 0.465 6.203 6445 Z= 0.239 Chirality : 0.037 0.125 707 Planarity : 0.004 0.040 834 Dihedral : 6.631 82.056 653 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.79 % Allowed : 15.52 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.74 (0.36), residues: 580 helix: 1.42 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.76 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 98 TYR 0.009 0.001 TYR A 161 PHE 0.007 0.001 PHE A 19 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4765) covalent geometry : angle 0.46219 ( 6411) SS BOND : bond 0.00258 ( 17) SS BOND : angle 0.87302 ( 34) hydrogen bonds : bond 0.03539 ( 261) hydrogen bonds : angle 3.30781 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7901 (mt-10) REVERT: A 104 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7304 (mm-40) REVERT: A 466 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7283 (mmtt) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.0679 time to fit residues: 4.4825 Evaluate side-chains 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 523 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.181985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115211 restraints weight = 4814.872| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.30 r_work: 0.2971 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4782 Z= 0.113 Angle : 0.477 6.251 6445 Z= 0.244 Chirality : 0.037 0.137 707 Planarity : 0.004 0.040 834 Dihedral : 6.590 81.448 653 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.77 % Allowed : 15.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.77 (0.36), residues: 580 helix: 1.45 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.77 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.010 0.001 TYR A 161 PHE 0.019 0.001 PHE A 49 TRP 0.003 0.001 TRP A 214 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4765) covalent geometry : angle 0.47331 ( 6411) SS BOND : bond 0.00252 ( 17) SS BOND : angle 0.93097 ( 34) hydrogen bonds : bond 0.03722 ( 261) hydrogen bonds : angle 3.29319 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.177 Fit side-chains REVERT: A 45 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 87 MET cc_start: 0.5804 (mmm) cc_final: 0.5499 (mmm) REVERT: A 104 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7304 (mm-40) REVERT: A 466 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7296 (mmtt) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.0658 time to fit residues: 4.6356 Evaluate side-chains 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 523 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116801 restraints weight = 4688.834| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.27 r_work: 0.3075 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4782 Z= 0.112 Angle : 0.485 6.218 6445 Z= 0.249 Chirality : 0.037 0.140 707 Planarity : 0.004 0.040 834 Dihedral : 6.524 80.468 653 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.38 % Allowed : 15.32 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.81 (0.37), residues: 580 helix: 1.49 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.75 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 98 TYR 0.010 0.001 TYR A 161 PHE 0.007 0.001 PHE A 19 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4765) covalent geometry : angle 0.48176 ( 6411) SS BOND : bond 0.00247 ( 17) SS BOND : angle 0.90298 ( 34) hydrogen bonds : bond 0.03665 ( 261) hydrogen bonds : angle 3.28421 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.187 Fit side-chains REVERT: A 45 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 87 MET cc_start: 0.5832 (mmm) cc_final: 0.5555 (mmm) REVERT: A 104 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7243 (mm-40) REVERT: A 466 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7345 (mmtt) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.0681 time to fit residues: 4.5476 Evaluate side-chains 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 523 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.0030 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.181980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128691 restraints weight = 4702.072| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.42 r_work: 0.2982 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4782 Z= 0.105 Angle : 0.476 6.225 6445 Z= 0.244 Chirality : 0.037 0.142 707 Planarity : 0.004 0.040 834 Dihedral : 6.360 79.049 653 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.18 % Allowed : 15.52 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.37), residues: 580 helix: 1.53 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.75 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 98 TYR 0.010 0.001 TYR A 161 PHE 0.019 0.001 PHE A 49 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4765) covalent geometry : angle 0.47337 ( 6411) SS BOND : bond 0.00233 ( 17) SS BOND : angle 0.85727 ( 34) hydrogen bonds : bond 0.03478 ( 261) hydrogen bonds : angle 3.23483 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.177 Fit side-chains REVERT: A 45 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7870 (mt-10) REVERT: A 87 MET cc_start: 0.5783 (mmm) cc_final: 0.5511 (mmm) REVERT: A 104 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7269 (mm-40) REVERT: A 466 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7740 (mtpt) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.0601 time to fit residues: 4.1305 Evaluate side-chains 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.0010 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.182281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115794 restraints weight = 4746.070| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.28 r_work: 0.2959 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4782 Z= 0.105 Angle : 0.476 6.222 6445 Z= 0.245 Chirality : 0.037 0.140 707 Planarity : 0.004 0.040 834 Dihedral : 6.306 78.750 653 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.98 % Allowed : 15.72 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.37), residues: 580 helix: 1.55 (0.27), residues: 403 sheet: None (None), residues: 0 loop : -1.74 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 98 TYR 0.009 0.001 TYR A 161 PHE 0.007 0.001 PHE A 19 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4765) covalent geometry : angle 0.47349 ( 6411) SS BOND : bond 0.00231 ( 17) SS BOND : angle 0.84707 ( 34) hydrogen bonds : bond 0.03482 ( 261) hydrogen bonds : angle 3.23007 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1310.49 seconds wall clock time: 23 minutes 3.23 seconds (1383.23 seconds total)