Starting phenix.real_space_refine on Wed Jul 23 23:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ym0_39393/07_2025/8ym0_39393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ym0_39393/07_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_39393/07_2025/8ym0_39393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ym0_39393/07_2025/8ym0_39393.map" model { file = "/net/cci-nas-00/data/ceres_data/8ym0_39393/07_2025/8ym0_39393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ym0_39393/07_2025/8ym0_39393.cif" } resolution = 3.05 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= 0.049 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.68, per 1000 atoms: 0.79 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: 1.30 Conformation dependent library (CDL) restraints added in 575.8 milliseconds 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: 0.51 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: 1.31 Time building geometry restraints manager: 1.41 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: 1.750 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- 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 (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: -0.56 (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 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 9 PHE 0.004 0.001 PHE A 149 TYR 0.018 0.001 TYR A 150 ARG 0.008 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.23967 ( 261) hydrogen bonds : angle 6.03230 ( 768) SS BOND : bond 0.00199 ( 17) SS BOND : angle 1.20989 ( 34) covalent geometry : bond 0.00297 ( 4765) covalent geometry : angle 0.50120 ( 6411) *********************** 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 : 0.484 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1798 time to fit residues: 12.5049 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 : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.182499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115912 restraints weight = 4666.161| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.33 r_work: 0.3057 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4782 Z= 0.124 Angle : 0.512 5.313 6445 Z= 0.266 Chirality : 0.037 0.122 707 Planarity : 0.004 0.042 834 Dihedral : 7.809 73.849 653 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.22 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 (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: 0.10 (0.36), residues: 580 helix: 0.83 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.68 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.006 0.001 HIS A 247 PHE 0.011 0.001 PHE A 149 TYR 0.021 0.001 TYR A 150 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 261) hydrogen bonds : angle 3.68661 ( 768) SS BOND : bond 0.00291 ( 17) SS BOND : angle 0.95767 ( 34) covalent geometry : bond 0.00289 ( 4765) covalent geometry : angle 0.50868 ( 6411) *********************** 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 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.534 Fit side-chains REVERT: A 104 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7455 (mm-40) REVERT: A 351 LYS cc_start: 0.7542 (mtpt) cc_final: 0.7151 (ttpt) REVERT: A 466 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7373 (mmtt) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.2048 time to fit residues: 12.7814 Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.181521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114902 restraints weight = 4635.615| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.27 r_work: 0.2987 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4782 Z= 0.133 Angle : 0.499 5.813 6445 Z= 0.257 Chirality : 0.038 0.126 707 Planarity : 0.004 0.042 834 Dihedral : 7.285 80.587 653 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.98 % Allowed : 10.61 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.42 (0.36), residues: 580 helix: 1.14 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.73 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 PHE 0.009 0.001 PHE A 149 TYR 0.013 0.001 TYR A 150 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 261) hydrogen bonds : angle 3.50869 ( 768) SS BOND : bond 0.00260 ( 17) SS BOND : angle 0.92680 ( 34) covalent geometry : bond 0.00328 ( 4765) covalent geometry : angle 0.49560 ( 6411) *********************** 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 51 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.495 Fit side-chains REVERT: A 45 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7989 (mt-10) REVERT: A 87 MET cc_start: 0.5695 (mmm) cc_final: 0.5443 (mmm) REVERT: A 104 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7405 (mm-40) REVERT: A 466 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7292 (mmtt) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1880 time to fit residues: 12.1697 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 : 0.490 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 33 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- 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 = 0.180628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113632 restraints weight = 4696.193| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.29 r_work: 0.3108 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4782 Z= 0.127 Angle : 0.489 5.935 6445 Z= 0.251 Chirality : 0.037 0.128 707 Planarity : 0.004 0.041 834 Dihedral : 7.008 81.732 653 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.38 % Allowed : 12.77 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.52 (0.36), residues: 580 helix: 1.23 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 PHE 0.017 0.001 PHE A 49 TYR 0.011 0.001 TYR A 150 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 261) hydrogen bonds : angle 3.41696 ( 768) SS BOND : bond 0.00278 ( 17) SS BOND : angle 0.91757 ( 34) covalent geometry : bond 0.00314 ( 4765) covalent geometry : angle 0.48542 ( 6411) *********************** 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 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.533 Fit side-chains REVERT: A 45 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 87 MET cc_start: 0.5761 (mmm) cc_final: 0.5464 (mmm) REVERT: A 104 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7369 (mm-40) REVERT: A 466 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7313 (mmtt) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.1648 time to fit residues: 10.8293 Evaluate side-chains 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.182212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115250 restraints weight = 4724.984| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.27 r_work: 0.2964 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1765 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= 0.111 Angle : 0.480 6.065 6445 Z= 0.247 Chirality : 0.037 0.137 707 Planarity : 0.004 0.041 834 Dihedral : 6.789 81.552 653 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.98 % Allowed : 14.34 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.65 (0.36), residues: 580 helix: 1.34 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.008 0.001 HIS A 247 PHE 0.007 0.001 PHE A 19 TYR 0.009 0.001 TYR A 370 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 261) hydrogen bonds : angle 3.36555 ( 768) SS BOND : bond 0.00271 ( 17) SS BOND : angle 0.96970 ( 34) covalent geometry : bond 0.00265 ( 4765) covalent geometry : angle 0.47622 ( 6411) *********************** 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 51 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7894 (mt-10) REVERT: A 104 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7303 (mm-40) REVERT: A 466 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7205 (mmtt) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1683 time to fit residues: 11.1498 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 : 0.497 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.182077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129425 restraints weight = 4687.673| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.70 r_work: 0.2971 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1828 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= 0.104 Angle : 0.468 6.111 6445 Z= 0.240 Chirality : 0.037 0.133 707 Planarity : 0.004 0.040 834 Dihedral : 6.531 80.079 653 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.79 % Allowed : 15.32 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.76 (0.37), residues: 580 helix: 1.44 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.008 0.001 HIS A 247 PHE 0.017 0.001 PHE A 49 TYR 0.009 0.001 TYR A 161 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 261) hydrogen bonds : angle 3.29852 ( 768) SS BOND : bond 0.00262 ( 17) SS BOND : angle 0.95208 ( 34) covalent geometry : bond 0.00246 ( 4765) covalent geometry : angle 0.46359 ( 6411) *********************** 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 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 104 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7261 (mm-40) REVERT: A 466 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7192 (mmtt) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1574 time to fit residues: 10.4457 Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 chunk 5 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.181410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128130 restraints weight = 4672.977| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.55 r_work: 0.2985 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1891 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= 0.112 Angle : 0.480 6.096 6445 Z= 0.246 Chirality : 0.037 0.138 707 Planarity : 0.004 0.040 834 Dihedral : 6.499 79.178 653 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.38 % Allowed : 15.52 % 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 (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: 0.79 (0.37), residues: 580 helix: 1.46 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.72 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.008 0.001 HIS A 247 PHE 0.007 0.001 PHE A 19 TYR 0.009 0.001 TYR A 161 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 261) hydrogen bonds : angle 3.28926 ( 768) SS BOND : bond 0.00252 ( 17) SS BOND : angle 0.95023 ( 34) covalent geometry : bond 0.00270 ( 4765) covalent geometry : angle 0.47677 ( 6411) *********************** 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 51 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.499 Fit side-chains REVERT: A 45 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 104 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7293 (mm-40) REVERT: A 466 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7279 (mmtt) outliers start: 7 outliers final: 7 residues processed: 50 average time/residue: 0.1485 time to fit residues: 10.1255 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 : 0.558 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 0.0040 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.4770 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.183541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122290 restraints weight = 4732.775| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.67 r_work: 0.3041 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.026 4782 Z= 0.095 Angle : 0.458 6.111 6445 Z= 0.235 Chirality : 0.036 0.136 707 Planarity : 0.004 0.040 834 Dihedral : 6.199 76.626 653 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.79 % Allowed : 16.31 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.88 (0.37), residues: 580 helix: 1.57 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.81 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.008 0.001 HIS A 247 PHE 0.019 0.001 PHE A 49 TYR 0.008 0.001 TYR A 161 ARG 0.007 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 261) hydrogen bonds : angle 3.20247 ( 768) SS BOND : bond 0.00223 ( 17) SS BOND : angle 0.84586 ( 34) covalent geometry : bond 0.00218 ( 4765) covalent geometry : angle 0.45474 ( 6411) *********************** 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 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.496 Fit side-chains REVERT: A 41 LYS cc_start: 0.7990 (ttpp) cc_final: 0.7590 (tttm) REVERT: A 45 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7881 (mt-10) REVERT: A 87 MET cc_start: 0.5739 (mmm) cc_final: 0.5436 (mmm) REVERT: A 104 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7286 (mm-40) REVERT: A 292 GLU cc_start: 0.7233 (pt0) cc_final: 0.6987 (pt0) REVERT: A 466 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7736 (mtpt) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.1654 time to fit residues: 10.8334 Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.180100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127065 restraints weight = 4705.650| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.73 r_work: 0.2937 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4782 Z= 0.160 Angle : 0.527 6.212 6445 Z= 0.268 Chirality : 0.039 0.141 707 Planarity : 0.004 0.040 834 Dihedral : 6.800 78.959 653 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.38 % Allowed : 15.91 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.36), residues: 580 helix: 1.34 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP A 214 HIS 0.009 0.001 HIS A 247 PHE 0.007 0.001 PHE A 19 TYR 0.012 0.002 TYR A 370 ARG 0.008 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 261) hydrogen bonds : angle 3.37785 ( 768) SS BOND : bond 0.00294 ( 17) SS BOND : angle 1.03949 ( 34) covalent geometry : bond 0.00406 ( 4765) covalent geometry : angle 0.52271 ( 6411) *********************** 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 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.637 Fit side-chains REVERT: A 87 MET cc_start: 0.5795 (mmm) cc_final: 0.5401 (mmm) REVERT: A 104 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7326 (mm-40) REVERT: A 466 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7295 (mmtt) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.2008 time to fit residues: 13.0545 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 : 0.609 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.180430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113442 restraints weight = 4717.700| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.29 r_work: 0.2983 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.003 0.033 4782 Z= 0.122 Angle : 0.489 6.171 6445 Z= 0.250 Chirality : 0.038 0.137 707 Planarity : 0.004 0.039 834 Dihedral : 6.561 78.379 653 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.98 % Allowed : 16.90 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.73 (0.37), residues: 580 helix: 1.41 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.72 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.008 0.001 HIS A 247 PHE 0.019 0.001 PHE A 49 TYR 0.010 0.001 TYR A 370 ARG 0.008 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 261) hydrogen bonds : angle 3.30048 ( 768) SS BOND : bond 0.00264 ( 17) SS BOND : angle 0.93485 ( 34) covalent geometry : bond 0.00299 ( 4765) covalent geometry : angle 0.48516 ( 6411) ********************** 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 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.551 Fit side-chains REVERT: A 45 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 104 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7372 (mm-40) REVERT: A 466 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7329 (mmtt) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1597 time to fit residues: 10.2080 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 : 0.493 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.179975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.112985 restraints weight = 4761.139| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.30 r_work: 0.2950 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4782 Z= 0.131 Angle : 0.502 6.241 6445 Z= 0.258 Chirality : 0.038 0.138 707 Planarity : 0.004 0.039 834 Dihedral : 6.625 78.514 653 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.98 % Allowed : 16.31 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.70 (0.36), residues: 580 helix: 1.39 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.74 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.008 0.001 HIS A 247 PHE 0.007 0.001 PHE A 19 TYR 0.011 0.001 TYR A 370 ARG 0.008 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 261) hydrogen bonds : angle 3.30558 ( 768) SS BOND : bond 0.00267 ( 17) SS BOND : angle 0.94885 ( 34) covalent geometry : bond 0.00323 ( 4765) covalent geometry : angle 0.49890 ( 6411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.16 seconds wall clock time: 53 minutes 19.48 seconds (3199.48 seconds total)