Starting phenix.real_space_refine on Sat May 10 02:09:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ym0_39393/05_2025/8ym0_39393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ym0_39393/05_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_39393/05_2025/8ym0_39393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ym0_39393/05_2025/8ym0_39393.map" model { file = "/net/cci-nas-00/data/ceres_data/8ym0_39393/05_2025/8ym0_39393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ym0_39393/05_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-5687/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: 3.42, per 1000 atoms: 0.73 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: 1.12 Conformation dependent library (CDL) restraints added in 646.8 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: 0.60 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: 1.22 Time building geometry restraints manager: 1.33 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: 0.800 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.130 ------------------------------------------------------------------------------- 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 : 0.509 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1768 time to fit residues: 12.3117 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 : 0.493 ------------------------------------------------------------------------------- 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: 0.9990 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 = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116005 restraints weight = 4666.160| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.31 r_work: 0.3058 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.521 Fit side-chains REVERT: A 104 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7453 (mm-40) REVERT: A 351 LYS cc_start: 0.7542 (mtpt) cc_final: 0.7150 (ttpt) REVERT: A 466 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7376 (mmtt) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.1971 time to fit residues: 12.2965 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 : 0.503 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.181248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115056 restraints weight = 4627.675| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.27 r_work: 0.3096 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1484 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= 0.122 Angle : 0.487 5.760 6445 Z= 0.251 Chirality : 0.037 0.122 707 Planarity : 0.004 0.042 834 Dihedral : 7.219 79.529 653 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.01 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 (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: 0.46 (0.36), residues: 580 helix: 1.16 (0.27), residues: 405 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 175 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 0.007 0.001 PHE A 149 TYR 0.013 0.001 TYR A 150 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 261) hydrogen bonds : angle 3.47635 ( 768) SS BOND : bond 0.00272 ( 17) SS BOND : angle 0.89106 ( 34) covalent geometry : bond 0.00296 ( 4765) covalent geometry : angle 0.48371 ( 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 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.547 Fit side-chains REVERT: A 45 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7986 (mt-10) REVERT: A 87 MET cc_start: 0.5675 (mmm) cc_final: 0.5427 (mmm) REVERT: A 104 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7436 (mm-40) REVERT: A 466 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7308 (mmtt) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1917 time to fit residues: 12.1710 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 : 0.592 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 10.0000 chunk 33 optimal weight: 0.0010 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.187996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135865 restraints weight = 4682.192| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.69 r_work: 0.2999 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4782 Z= 0.103 Angle : 0.462 5.906 6445 Z= 0.238 Chirality : 0.036 0.117 707 Planarity : 0.004 0.041 834 Dihedral : 6.709 80.108 653 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 : 0.59 % Allowed : 13.16 % Favored : 86.25 % 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 (0.37), residues: 580 helix: 1.35 (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 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 247 PHE 0.016 0.001 PHE A 49 TYR 0.009 0.001 TYR A 150 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 261) hydrogen bonds : angle 3.32627 ( 768) SS BOND : bond 0.00254 ( 17) SS BOND : angle 0.82269 ( 34) covalent geometry : bond 0.00242 ( 4765) covalent geometry : angle 0.45983 ( 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 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.497 Fit side-chains REVERT: A 45 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 87 MET cc_start: 0.5644 (mmm) cc_final: 0.5360 (mmm) REVERT: A 104 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7314 (mm-40) REVERT: A 466 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7250 (mmtt) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 0.1760 time to fit residues: 10.9354 Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU 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: 3.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 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 = 0.182204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115918 restraints weight = 4718.554| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.25 r_work: 0.3130 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1725 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 6.008 6445 Z= 0.245 Chirality : 0.037 0.120 707 Planarity : 0.004 0.041 834 Dihedral : 6.666 80.398 653 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.98 % Allowed : 14.15 % Favored : 84.87 % 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 (0.37), residues: 580 helix: 1.39 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.76 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.009 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 0.03770 ( 261) hydrogen bonds : angle 3.33237 ( 768) SS BOND : bond 0.00266 ( 17) SS BOND : angle 1.01446 ( 34) covalent geometry : bond 0.00272 ( 4765) covalent geometry : angle 0.47300 ( 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 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 87 MET cc_start: 0.5677 (mmm) cc_final: 0.5401 (mmm) REVERT: A 104 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7356 (mm-40) REVERT: A 466 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7324 (mmtt) outliers start: 5 outliers final: 5 residues processed: 49 average time/residue: 0.1747 time to fit residues: 11.3302 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 : 0.559 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.181813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115172 restraints weight = 4697.615| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.27 r_work: 0.3064 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1791 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= 0.126 Angle : 0.491 6.069 6445 Z= 0.251 Chirality : 0.037 0.132 707 Planarity : 0.004 0.040 834 Dihedral : 6.702 80.213 653 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.38 % Allowed : 14.54 % Favored : 84.09 % 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: 0.71 (0.37), residues: 580 helix: 1.40 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.76 (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 0.020 0.001 PHE A 49 TYR 0.010 0.001 TYR A 370 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 261) hydrogen bonds : angle 3.35904 ( 768) SS BOND : bond 0.00273 ( 17) SS BOND : angle 1.00203 ( 34) covalent geometry : bond 0.00310 ( 4765) covalent geometry : angle 0.48640 ( 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 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.517 Fit side-chains REVERT: A 45 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7924 (mt-10) REVERT: A 104 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7365 (mm-40) REVERT: A 466 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7313 (mmtt) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.1541 time to fit residues: 9.9524 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 : 0.534 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.183799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130780 restraints weight = 4661.466| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.38 r_work: 0.3059 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4782 Z= 0.091 Angle : 0.454 5.976 6445 Z= 0.233 Chirality : 0.036 0.141 707 Planarity : 0.003 0.040 834 Dihedral : 6.203 77.472 653 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.98 % Allowed : 15.13 % 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: 0.90 (0.37), residues: 580 helix: 1.56 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.75 (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 0.006 0.001 PHE A 19 TYR 0.008 0.001 TYR A 161 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 261) hydrogen bonds : angle 3.20107 ( 768) SS BOND : bond 0.00226 ( 17) SS BOND : angle 0.80241 ( 34) covalent geometry : bond 0.00203 ( 4765) covalent geometry : angle 0.45185 ( 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 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.544 Fit side-chains REVERT: A 41 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7569 (tttm) REVERT: A 45 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7903 (mt-10) REVERT: A 87 MET cc_start: 0.5726 (mmm) cc_final: 0.5444 (mmm) REVERT: A 104 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7254 (mm-40) REVERT: A 292 GLU cc_start: 0.7257 (pt0) cc_final: 0.7005 (pt0) REVERT: A 466 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7719 (mtpt) outliers start: 5 outliers final: 5 residues processed: 49 average time/residue: 0.1710 time to fit residues: 11.1945 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 : 0.534 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 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 = 0.3941 r_free = 0.3941 target = 0.181869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121460 restraints weight = 4735.153| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.57 r_work: 0.3017 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1903 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= 0.123 Angle : 0.488 6.118 6445 Z= 0.249 Chirality : 0.037 0.131 707 Planarity : 0.004 0.040 834 Dihedral : 6.421 77.513 653 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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 (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: 0.82 (0.37), residues: 580 helix: 1.50 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.76 (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 0.023 0.001 PHE A 49 TYR 0.010 0.001 TYR A 161 ARG 0.007 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 261) hydrogen bonds : angle 3.26041 ( 768) SS BOND : bond 0.00261 ( 17) SS BOND : angle 0.91189 ( 34) covalent geometry : bond 0.00301 ( 4765) covalent geometry : angle 0.48456 ( 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 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.559 Fit side-chains REVERT: A 41 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7647 (tttm) REVERT: A 45 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 104 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7319 (mm-40) REVERT: A 466 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7324 (mmtt) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.1677 time to fit residues: 10.3380 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 : 0.488 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 376 GLU 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: 6.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.178546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116045 restraints weight = 4695.613| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.78 r_work: 0.2968 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4782 Z= 0.152 Angle : 0.522 6.216 6445 Z= 0.266 Chirality : 0.039 0.137 707 Planarity : 0.004 0.040 834 Dihedral : 6.822 79.176 653 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.18 % Allowed : 15.32 % Favored : 83.50 % 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: 0.69 (0.36), residues: 580 helix: 1.35 (0.27), residues: 405 sheet: None (None), residues: 0 loop : -1.70 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP A 214 HIS 0.008 0.001 HIS A 247 PHE 0.007 0.001 PHE A 19 TYR 0.012 0.001 TYR A 370 ARG 0.007 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 261) hydrogen bonds : angle 3.37862 ( 768) SS BOND : bond 0.00300 ( 17) SS BOND : angle 1.01552 ( 34) covalent geometry : bond 0.00384 ( 4765) covalent geometry : angle 0.51843 ( 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 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.502 Fit side-chains REVERT: A 104 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7389 (mm-40) REVERT: A 466 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7316 (mmtt) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.1600 time to fit residues: 10.2623 Evaluate side-chains 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.182176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115720 restraints weight = 4713.585| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.28 r_work: 0.2994 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2006 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= 0.104 Angle : 0.476 6.072 6445 Z= 0.246 Chirality : 0.037 0.123 707 Planarity : 0.004 0.040 834 Dihedral : 6.386 77.182 653 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.37), residues: 580 helix: 1.55 (0.27), residues: 403 sheet: None (None), residues: 0 loop : -1.77 (0.45), residues: 177 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 0.018 0.001 PHE A 49 TYR 0.009 0.001 TYR A 161 ARG 0.008 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 261) hydrogen bonds : angle 3.24225 ( 768) SS BOND : bond 0.00234 ( 17) SS BOND : angle 0.86176 ( 34) covalent geometry : bond 0.00244 ( 4765) covalent geometry : angle 0.47334 ( 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 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.543 Fit side-chains REVERT: A 41 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7625 (tttm) REVERT: A 45 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7924 (mt-10) REVERT: A 104 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7339 (mm-40) REVERT: A 466 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7707 (mtpt) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.1753 time to fit residues: 10.6956 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 : 0.567 ------------------------------------------------------------------------------- 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 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.174632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106708 restraints weight = 4758.580| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.34 r_work: 0.2871 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 4782 Z= 0.265 Angle : 0.632 6.642 6445 Z= 0.320 Chirality : 0.044 0.163 707 Planarity : 0.005 0.043 834 Dihedral : 7.412 83.574 653 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.18 % Allowed : 14.93 % 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: 0.32 (0.36), residues: 580 helix: 1.08 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 214 HIS 0.011 0.002 HIS A 247 PHE 0.010 0.002 PHE A 228 TYR 0.017 0.002 TYR A 370 ARG 0.008 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.05766 ( 261) hydrogen bonds : angle 3.59626 ( 768) SS BOND : bond 0.00417 ( 17) SS BOND : angle 1.28535 ( 34) covalent geometry : bond 0.00686 ( 4765) covalent geometry : angle 0.62627 ( 6411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2803.57 seconds wall clock time: 49 minutes 10.23 seconds (2950.23 seconds total)