Starting phenix.real_space_refine on Fri Aug 22 15:03:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ylx_39392/08_2025/8ylx_39392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ylx_39392/08_2025/8ylx_39392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ylx_39392/08_2025/8ylx_39392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ylx_39392/08_2025/8ylx_39392.map" model { file = "/net/cci-nas-00/data/ceres_data/8ylx_39392/08_2025/8ylx_39392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ylx_39392/08_2025/8ylx_39392.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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 2947 2.51 5 N 783 2.21 5 O 889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4660 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'OCA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.21, per 1000 atoms: 0.26 Number of scatterers: 4660 At special positions: 0 Unit cell: (69.72, 94.08, 96.6, 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 889 8.00 N 783 7.00 C 2947 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 130.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.549A pdb=" N LYS A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 56 removed outlier: 3.609A pdb=" N HIS A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.581A pdb=" N THR A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.555A pdb=" N GLU A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.504A pdb=" N LEU A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.855A pdb=" N PHE A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.775A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 4.158A pdb=" N GLU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.671A pdb=" N GLN A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 223 removed outlier: 3.769A pdb=" N PHE A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.644A pdb=" N GLU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 3.516A pdb=" N ALA A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.650A pdb=" N ILE A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.899A pdb=" N LYS A 281 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 4.146A pdb=" N SER A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.902A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.641A 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: 4.543A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.814A pdb=" N GLN A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 415 removed outlier: 4.080A pdb=" N LYS A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.588A pdb=" N CYS A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.865A pdb=" N CYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.503A 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: 3.780A pdb=" N THR A 508 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.948A 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 561 removed outlier: 3.711A pdb=" N ASP A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS A 558 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 582 254 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1347 1.33 - 1.46: 757 1.46 - 1.58: 2596 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4747 Sorted by residual: bond pdb=" N CYS A 437 " pdb=" CA CYS A 437 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.63e+00 bond pdb=" N ILE A 513 " pdb=" CA ILE A 513 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.54e+00 bond pdb=" N CYS A 438 " pdb=" CA CYS A 438 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.31e-02 5.83e+03 5.00e+00 bond pdb=" C LYS A 536 " pdb=" O LYS A 536 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.49e+00 bond pdb=" N GLU A 95 " pdb=" CA GLU A 95 " ideal model delta sigma weight residual 1.451 1.484 -0.034 1.60e-02 3.91e+03 4.40e+00 ... (remaining 4742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 6149 1.51 - 3.03: 191 3.03 - 4.54: 41 4.54 - 6.06: 10 6.06 - 7.57: 2 Bond angle restraints: 6393 Sorted by residual: angle pdb=" N CYS A 438 " pdb=" CA CYS A 438 " pdb=" C CYS A 438 " ideal model delta sigma weight residual 113.18 106.71 6.47 1.21e+00 6.83e-01 2.86e+01 angle pdb=" C LYS A 436 " pdb=" N CYS A 437 " pdb=" CA CYS A 437 " ideal model delta sigma weight residual 122.50 114.93 7.57 1.82e+00 3.02e-01 1.73e+01 angle pdb=" N THR A 540 " pdb=" CA THR A 540 " pdb=" CB THR A 540 " ideal model delta sigma weight residual 111.51 105.88 5.63 1.48e+00 4.57e-01 1.45e+01 angle pdb=" C ASP A 512 " pdb=" CA ASP A 512 " pdb=" CB ASP A 512 " ideal model delta sigma weight residual 116.54 112.17 4.37 1.15e+00 7.56e-01 1.44e+01 angle pdb=" CA GLU A 95 " pdb=" C GLU A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 117.44 121.36 -3.92 1.13e+00 7.83e-01 1.20e+01 ... (remaining 6388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 2612 17.72 - 35.44: 312 35.44 - 53.16: 53 53.16 - 70.88: 14 70.88 - 88.59: 9 Dihedral angle restraints: 3000 sinusoidal: 1261 harmonic: 1739 Sorted by residual: 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 -174.59 88.59 1 1.00e+01 1.00e-02 9.36e+01 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 -173.46 87.46 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A 392 " pdb=" SG CYS A 392 " pdb=" SG CYS A 438 " pdb=" CB CYS A 438 " ideal model delta sinusoidal sigma weight residual 93.00 178.39 -85.39 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 2997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 427 0.033 - 0.067: 217 0.067 - 0.100: 44 0.100 - 0.133: 16 0.133 - 0.167: 3 Chirality restraints: 707 Sorted by residual: chirality pdb=" CA ILE A 513 " pdb=" N ILE A 513 " pdb=" C ILE A 513 " pdb=" CB ILE A 513 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 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 2.68 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA THR A 540 " pdb=" N THR A 540 " pdb=" C THR A 540 " pdb=" CB THR A 540 " both_signs ideal model delta sigma weight residual False 2.53 2.66 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 704 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 536 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO A 537 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 446 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 447 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 536 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C LYS A 536 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS A 536 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO A 537 " -0.011 2.00e-02 2.50e+03 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 685 2.75 - 3.29: 4470 3.29 - 3.83: 7227 3.83 - 4.36: 8635 4.36 - 4.90: 14984 Nonbonded interactions: 36001 Sorted by model distance: nonbonded pdb=" O CYS A 34 " pdb=" OH TYR A 140 " model vdw 2.213 3.040 nonbonded pdb=" OE2 GLU A 230 " pdb=" OH TYR A 263 " model vdw 2.254 3.040 nonbonded pdb=" O GLU A 505 " pdb=" OG1 THR A 508 " model vdw 2.313 3.040 nonbonded pdb=" O ASP A 72 " pdb=" OG1 THR A 76 " model vdw 2.315 3.040 nonbonded pdb=" OG SER A 312 " pdb=" OD1 ASP A 314 " model vdw 2.357 3.040 ... (remaining 35996 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: 0.960 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.005 0.048 4764 Z= 0.230 Angle : 0.677 7.570 6427 Z= 0.389 Chirality : 0.042 0.167 707 Planarity : 0.005 0.064 832 Dihedral : 15.303 80.548 1809 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 0.59 % Allowed : 0.98 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.34), residues: 580 helix: -0.88 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -1.64 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 348 TYR 0.025 0.002 TYR A 150 PHE 0.016 0.001 PHE A 551 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 4747) covalent geometry : angle 0.67111 ( 6393) SS BOND : bond 0.00302 ( 17) SS BOND : angle 1.41686 ( 34) hydrogen bonds : bond 0.26082 ( 254) hydrogen bonds : angle 7.60810 ( 744) *********************** 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 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.111 Fit side-chains REVERT: A 33 GLN cc_start: 0.8498 (mt0) cc_final: 0.8123 (mt0) outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.0850 time to fit residues: 5.0178 Evaluate side-chains 34 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.182823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134846 restraints weight = 4943.830| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.47 r_work: 0.2953 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4764 Z= 0.128 Angle : 0.519 4.830 6427 Z= 0.276 Chirality : 0.038 0.119 707 Planarity : 0.004 0.053 832 Dihedral : 6.446 63.887 641 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 0.79 % Allowed : 6.48 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.36), residues: 580 helix: 0.40 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.78 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.018 0.001 TYR A 150 PHE 0.012 0.001 PHE A 488 TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4747) covalent geometry : angle 0.51603 ( 6393) SS BOND : bond 0.00232 ( 17) SS BOND : angle 0.90769 ( 34) hydrogen bonds : bond 0.04475 ( 254) hydrogen bonds : angle 4.08061 ( 744) *********************** 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 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.212 Fit side-chains REVERT: A 16 GLU cc_start: 0.7875 (tp30) cc_final: 0.7641 (tp30) REVERT: A 519 LYS cc_start: 0.7973 (tttp) cc_final: 0.7210 (tmtt) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.0701 time to fit residues: 4.2800 Evaluate side-chains 38 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 471 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.0370 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.184962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135638 restraints weight = 4937.529| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.11 r_work: 0.2972 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4764 Z= 0.106 Angle : 0.485 5.940 6427 Z= 0.255 Chirality : 0.037 0.123 707 Planarity : 0.004 0.047 832 Dihedral : 6.185 56.149 641 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.59 % Rotamer: Outliers : 0.98 % Allowed : 10.41 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.37), residues: 580 helix: 0.87 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.73 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.010 0.001 TYR A 150 PHE 0.023 0.001 PHE A 49 TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4747) covalent geometry : angle 0.47698 ( 6393) SS BOND : bond 0.00192 ( 17) SS BOND : angle 1.29983 ( 34) hydrogen bonds : bond 0.03740 ( 254) hydrogen bonds : angle 3.60408 ( 744) *********************** 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 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.157 Fit side-chains REVERT: A 16 GLU cc_start: 0.7812 (tp30) cc_final: 0.7536 (tp30) REVERT: A 519 LYS cc_start: 0.8055 (tttp) cc_final: 0.7385 (tmtt) outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.0617 time to fit residues: 3.7389 Evaluate side-chains 40 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 467 THR 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 6 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.184092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135429 restraints weight = 4921.995| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.13 r_work: 0.2957 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4764 Z= 0.131 Angle : 0.516 6.060 6427 Z= 0.271 Chirality : 0.039 0.171 707 Planarity : 0.004 0.042 832 Dihedral : 6.159 56.198 641 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 1.57 % Allowed : 12.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.37), residues: 580 helix: 0.86 (0.27), residues: 406 sheet: None (None), residues: 0 loop : -1.56 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.011 0.001 TYR A 150 PHE 0.016 0.001 PHE A 488 TRP 0.001 0.001 TRP A 214 HIS 0.005 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4747) covalent geometry : angle 0.50654 ( 6393) SS BOND : bond 0.00265 ( 17) SS BOND : angle 1.44151 ( 34) hydrogen bonds : bond 0.04070 ( 254) hydrogen bonds : angle 3.63591 ( 744) *********************** 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 52 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7745 (tp30) cc_final: 0.7419 (tp30) REVERT: A 466 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7599 (mttp) REVERT: A 519 LYS cc_start: 0.8030 (tttp) cc_final: 0.7239 (tmtt) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.0707 time to fit residues: 4.3975 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 467 THR 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 37 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.182268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133393 restraints weight = 4911.450| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.57 r_work: 0.3149 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4764 Z= 0.123 Angle : 0.506 5.282 6427 Z= 0.263 Chirality : 0.038 0.157 707 Planarity : 0.004 0.037 832 Dihedral : 5.977 55.477 641 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % Rotamer: Outliers : 1.57 % Allowed : 12.97 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.37), residues: 580 helix: 0.94 (0.27), residues: 407 sheet: None (None), residues: 0 loop : -1.58 (0.51), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.009 0.001 TYR A 161 PHE 0.024 0.001 PHE A 49 TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4747) covalent geometry : angle 0.49861 ( 6393) SS BOND : bond 0.00227 ( 17) SS BOND : angle 1.30539 ( 34) hydrogen bonds : bond 0.03790 ( 254) hydrogen bonds : angle 3.46686 ( 744) *********************** 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 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.179 Fit side-chains REVERT: A 16 GLU cc_start: 0.7774 (tp30) cc_final: 0.7472 (tp30) REVERT: A 245 CYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8607 (m) REVERT: A 487 CYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6333 (t) REVERT: A 519 LYS cc_start: 0.8087 (tttp) cc_final: 0.7436 (tmtt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.0637 time to fit residues: 4.0506 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.0020 chunk 2 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.182478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134231 restraints weight = 4990.867| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.50 r_work: 0.2975 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4764 Z= 0.114 Angle : 0.495 6.091 6427 Z= 0.258 Chirality : 0.038 0.168 707 Planarity : 0.004 0.051 832 Dihedral : 5.863 55.834 641 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 1.57 % Allowed : 14.34 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.37), residues: 580 helix: 1.09 (0.27), residues: 407 sheet: None (None), residues: 0 loop : -1.58 (0.51), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.009 0.001 TYR A 161 PHE 0.013 0.001 PHE A 488 TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4747) covalent geometry : angle 0.48860 ( 6393) SS BOND : bond 0.00259 ( 17) SS BOND : angle 1.20775 ( 34) hydrogen bonds : bond 0.03607 ( 254) hydrogen bonds : angle 3.37201 ( 744) *********************** 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 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.108 Fit side-chains REVERT: A 245 CYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 487 CYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6003 (t) REVERT: A 519 LYS cc_start: 0.8008 (tttp) cc_final: 0.7284 (tmtt) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.0490 time to fit residues: 3.3199 Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.185587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136494 restraints weight = 4942.682| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.56 r_work: 0.3164 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4764 Z= 0.105 Angle : 0.486 6.621 6427 Z= 0.251 Chirality : 0.038 0.153 707 Planarity : 0.004 0.049 832 Dihedral : 5.675 58.080 641 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 1.57 % Allowed : 15.32 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.38), residues: 580 helix: 1.21 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.54 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 521 TYR 0.008 0.001 TYR A 161 PHE 0.027 0.001 PHE A 49 TRP 0.001 0.001 TRP A 214 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4747) covalent geometry : angle 0.47998 ( 6393) SS BOND : bond 0.00210 ( 17) SS BOND : angle 1.12102 ( 34) hydrogen bonds : bond 0.03354 ( 254) hydrogen bonds : angle 3.28425 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.149 Fit side-chains REVERT: A 245 CYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8576 (m) REVERT: A 487 CYS cc_start: 0.6832 (OUTLIER) cc_final: 0.5994 (t) REVERT: A 519 LYS cc_start: 0.7986 (tttp) cc_final: 0.7287 (tmtt) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.0570 time to fit residues: 3.6475 Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.184081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135964 restraints weight = 5033.856| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.47 r_work: 0.2988 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4764 Z= 0.103 Angle : 0.485 7.288 6427 Z= 0.250 Chirality : 0.038 0.155 707 Planarity : 0.004 0.051 832 Dihedral : 5.514 58.534 641 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.59 % Rotamer: Outliers : 1.57 % Allowed : 15.52 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.37), residues: 580 helix: 1.28 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.61 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.008 0.001 TYR A 161 PHE 0.011 0.001 PHE A 488 TRP 0.001 0.000 TRP A 214 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4747) covalent geometry : angle 0.47920 ( 6393) SS BOND : bond 0.00209 ( 17) SS BOND : angle 1.11101 ( 34) hydrogen bonds : bond 0.03276 ( 254) hydrogen bonds : angle 3.23409 ( 744) *********************** 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 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.162 Fit side-chains REVERT: A 245 CYS cc_start: 0.8901 (OUTLIER) cc_final: 0.7987 (t) REVERT: A 487 CYS cc_start: 0.6831 (OUTLIER) cc_final: 0.5967 (t) REVERT: A 519 LYS cc_start: 0.7841 (tttp) cc_final: 0.7111 (tmtt) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.0520 time to fit residues: 3.1184 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.0570 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.183136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134709 restraints weight = 4908.437| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.20 r_work: 0.2979 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4764 Z= 0.111 Angle : 0.483 6.099 6427 Z= 0.252 Chirality : 0.038 0.153 707 Planarity : 0.004 0.052 832 Dihedral : 5.376 53.216 641 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % 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 : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.37), residues: 580 helix: 1.32 (0.27), residues: 402 sheet: None (None), residues: 0 loop : -1.61 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.008 0.001 TYR A 161 PHE 0.012 0.001 PHE A 488 TRP 0.001 0.000 TRP A 214 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4747) covalent geometry : angle 0.47696 ( 6393) SS BOND : bond 0.00206 ( 17) SS BOND : angle 1.15362 ( 34) hydrogen bonds : bond 0.03488 ( 254) hydrogen bonds : angle 3.26750 ( 744) *********************** 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 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.119 Fit side-chains REVERT: A 245 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8031 (t) REVERT: A 487 CYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6053 (t) REVERT: A 519 LYS cc_start: 0.7757 (tttp) cc_final: 0.7025 (tmtt) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.0519 time to fit residues: 3.0332 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.183568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135980 restraints weight = 4958.995| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.41 r_work: 0.3199 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4764 Z= 0.107 Angle : 0.478 6.041 6427 Z= 0.248 Chirality : 0.037 0.150 707 Planarity : 0.004 0.050 832 Dihedral : 5.032 43.209 641 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % 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 : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.38), residues: 580 helix: 1.35 (0.27), residues: 404 sheet: None (None), residues: 0 loop : -1.56 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.008 0.001 TYR A 161 PHE 0.011 0.001 PHE A 488 TRP 0.001 0.000 TRP A 214 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4747) covalent geometry : angle 0.47196 ( 6393) SS BOND : bond 0.00207 ( 17) SS BOND : angle 1.13614 ( 34) hydrogen bonds : bond 0.03372 ( 254) hydrogen bonds : angle 3.24026 ( 744) ********************** 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 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.120 Fit side-chains REVERT: A 245 CYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8012 (t) REVERT: A 487 CYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6062 (t) REVERT: A 519 LYS cc_start: 0.7861 (tttp) cc_final: 0.7171 (tmtt) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.0594 time to fit residues: 3.5519 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.186695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138314 restraints weight = 4914.958| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.07 r_work: 0.3022 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4764 Z= 0.091 Angle : 0.459 5.612 6427 Z= 0.239 Chirality : 0.036 0.136 707 Planarity : 0.004 0.049 832 Dihedral : 4.665 32.338 641 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 1.77 % Allowed : 15.72 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.38), residues: 580 helix: 1.47 (0.28), residues: 404 sheet: None (None), residues: 0 loop : -1.55 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.008 0.001 TYR A 30 PHE 0.012 0.001 PHE A 488 TRP 0.002 0.000 TRP A 214 HIS 0.003 0.000 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 4747) covalent geometry : angle 0.45381 ( 6393) SS BOND : bond 0.00220 ( 17) SS BOND : angle 1.03894 ( 34) hydrogen bonds : bond 0.02915 ( 254) hydrogen bonds : angle 3.12496 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1086.97 seconds wall clock time: 19 minutes 15.87 seconds (1155.87 seconds total)