Starting phenix.real_space_refine on Wed Jul 23 23:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ylx_39392/07_2025/8ylx_39392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ylx_39392/07_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_39392/07_2025/8ylx_39392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ylx_39392/07_2025/8ylx_39392.map" model { file = "/net/cci-nas-00/data/ceres_data/8ylx_39392/07_2025/8ylx_39392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ylx_39392/07_2025/8ylx_39392.cif" } resolution = 3.18 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= 0.044 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.07, per 1000 atoms: 0.66 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: 1.05 Conformation dependent library (CDL) restraints added in 518.7 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: 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: 0.44 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: 1.08 Time building geometry restraints manager: 1.28 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: 0.550 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (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 TRP 0.002 0.001 TRP A 214 HIS 0.007 0.001 HIS A 510 PHE 0.016 0.001 PHE A 551 TYR 0.025 0.002 TYR A 150 ARG 0.005 0.001 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.26082 ( 254) hydrogen bonds : angle 7.60810 ( 744) SS BOND : bond 0.00302 ( 17) SS BOND : angle 1.41686 ( 34) covalent geometry : bond 0.00530 ( 4747) covalent geometry : angle 0.67111 ( 6393) *********************** 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 : 0.504 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: 0.2201 time to fit residues: 13.2466 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 : 0.534 ------------------------------------------------------------------------------- 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: 0.8980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.183676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135901 restraints weight = 4897.326| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.11 r_work: 0.2982 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4764 Z= 0.122 Angle : 0.511 4.833 6427 Z= 0.273 Chirality : 0.038 0.125 707 Planarity : 0.004 0.052 832 Dihedral : 6.342 62.068 641 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % Rotamer: Outliers : 0.79 % Allowed : 6.09 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.36), residues: 580 helix: 0.50 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -1.78 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.005 0.001 HIS A 510 PHE 0.010 0.001 PHE A 488 TYR 0.017 0.001 TYR A 150 ARG 0.003 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 254) hydrogen bonds : angle 4.05344 ( 744) SS BOND : bond 0.00217 ( 17) SS BOND : angle 0.87556 ( 34) covalent geometry : bond 0.00278 ( 4747) covalent geometry : angle 0.50800 ( 6393) *********************** 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 : 0.547 Fit side-chains REVERT: A 16 GLU cc_start: 0.7883 (tp30) cc_final: 0.7650 (tp30) REVERT: A 519 LYS cc_start: 0.7987 (tttp) cc_final: 0.7234 (tmtt) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.1804 time to fit residues: 10.9999 Evaluate side-chains 37 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 5 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.183042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134283 restraints weight = 4893.725| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.12 r_work: 0.2943 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4764 Z= 0.126 Angle : 0.502 4.970 6427 Z= 0.264 Chirality : 0.038 0.129 707 Planarity : 0.004 0.047 832 Dihedral : 6.325 58.029 641 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.59 % Rotamer: Outliers : 0.98 % Allowed : 10.81 % Favored : 88.21 % 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: 0.05 (0.37), residues: 580 helix: 0.83 (0.27), residues: 399 sheet: None (None), residues: 0 loop : -1.72 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 510 PHE 0.023 0.001 PHE A 49 TYR 0.013 0.001 TYR A 150 ARG 0.003 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 254) hydrogen bonds : angle 3.66416 ( 744) SS BOND : bond 0.00256 ( 17) SS BOND : angle 1.21713 ( 34) covalent geometry : bond 0.00308 ( 4747) covalent geometry : angle 0.49540 ( 6393) *********************** 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 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.506 Fit side-chains REVERT: A 16 GLU cc_start: 0.7824 (tp30) cc_final: 0.7552 (tp30) REVERT: A 519 LYS cc_start: 0.8023 (tttp) cc_final: 0.7361 (tmtt) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.1725 time to fit residues: 10.4601 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 : 0.443 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.183920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135112 restraints weight = 4962.574| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.24 r_work: 0.2979 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4764 Z= 0.135 Angle : 0.526 6.667 6427 Z= 0.277 Chirality : 0.039 0.178 707 Planarity : 0.004 0.042 832 Dihedral : 6.151 58.214 641 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 1.18 % Allowed : 11.98 % Favored : 86.84 % 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: 0.16 (0.37), residues: 580 helix: 0.83 (0.27), residues: 406 sheet: None (None), residues: 0 loop : -1.55 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.005 0.001 HIS A 247 PHE 0.017 0.001 PHE A 488 TYR 0.011 0.001 TYR A 150 ARG 0.003 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 254) hydrogen bonds : angle 3.63709 ( 744) SS BOND : bond 0.00253 ( 17) SS BOND : angle 1.49957 ( 34) covalent geometry : bond 0.00337 ( 4747) covalent geometry : angle 0.51633 ( 6393) *********************** 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: 6 poor density : 42 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7776 (tp30) cc_final: 0.7445 (tp30) REVERT: A 466 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7615 (mttp) REVERT: A 519 LYS cc_start: 0.8046 (tttp) cc_final: 0.7268 (tmtt) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1606 time to fit residues: 10.2197 Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.182712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133877 restraints weight = 4942.751| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.33 r_work: 0.3098 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4764 Z= 0.135 Angle : 0.514 5.582 6427 Z= 0.268 Chirality : 0.039 0.167 707 Planarity : 0.004 0.037 832 Dihedral : 6.103 59.427 641 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.59 % Rotamer: Outliers : 1.77 % Allowed : 13.36 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.22 (0.37), residues: 580 helix: 0.97 (0.27), residues: 402 sheet: None (None), residues: 0 loop : -1.76 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.005 0.001 HIS A 247 PHE 0.024 0.001 PHE A 49 TYR 0.010 0.001 TYR A 150 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 254) hydrogen bonds : angle 3.51373 ( 744) SS BOND : bond 0.00250 ( 17) SS BOND : angle 1.34178 ( 34) covalent geometry : bond 0.00338 ( 4747) covalent geometry : angle 0.50622 ( 6393) *********************** 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 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7853 (tp30) cc_final: 0.7567 (tp30) REVERT: A 487 CYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6279 (t) REVERT: A 519 LYS cc_start: 0.8094 (tttp) cc_final: 0.7459 (tmtt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1481 time to fit residues: 9.7749 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 : 0.543 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.183156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.135374 restraints weight = 4875.823| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.59 r_work: 0.2994 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2293 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= 0.104 Angle : 0.480 6.103 6427 Z= 0.250 Chirality : 0.038 0.167 707 Planarity : 0.004 0.054 832 Dihedral : 5.850 56.895 641 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.59 % 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 : 0.18 % 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: 0.43 (0.37), residues: 580 helix: 1.08 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.63 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 247 PHE 0.012 0.001 PHE A 488 TYR 0.008 0.001 TYR A 161 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 254) hydrogen bonds : angle 3.33840 ( 744) SS BOND : bond 0.00203 ( 17) SS BOND : angle 1.14714 ( 34) covalent geometry : bond 0.00245 ( 4747) covalent geometry : angle 0.47347 ( 6393) *********************** 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 : 0.494 Fit side-chains REVERT: A 245 CYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8758 (m) REVERT: A 487 CYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6345 (t) REVERT: A 519 LYS cc_start: 0.7985 (tttp) cc_final: 0.7257 (tmtt) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.1496 time to fit residues: 9.7126 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 : 0.529 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.178574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130877 restraints weight = 4904.598| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.22 r_work: 0.2902 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4764 Z= 0.170 Angle : 0.547 6.909 6427 Z= 0.283 Chirality : 0.041 0.182 707 Planarity : 0.004 0.051 832 Dihedral : 6.173 58.695 641 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 1.77 % Allowed : 15.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.28 (0.37), residues: 580 helix: 1.03 (0.27), residues: 403 sheet: None (None), residues: 0 loop : -1.77 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.006 0.001 HIS A 247 PHE 0.024 0.002 PHE A 49 TYR 0.011 0.002 TYR A 161 ARG 0.003 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 254) hydrogen bonds : angle 3.54752 ( 744) SS BOND : bond 0.00283 ( 17) SS BOND : angle 1.38123 ( 34) covalent geometry : bond 0.00435 ( 4747) covalent geometry : angle 0.53914 ( 6393) *********************** 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: 9 poor density : 41 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 LYS cc_start: 0.7878 (tttp) cc_final: 0.7216 (tmtt) outliers start: 9 outliers final: 8 residues processed: 49 average time/residue: 0.1618 time to fit residues: 10.7571 Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 467 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.179275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131409 restraints weight = 4910.042| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.24 r_work: 0.2916 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4764 Z= 0.152 Angle : 0.538 7.864 6427 Z= 0.280 Chirality : 0.040 0.179 707 Planarity : 0.004 0.052 832 Dihedral : 6.125 55.910 641 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % 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 (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: 0.28 (0.37), residues: 580 helix: 0.94 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.59 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.006 0.001 HIS A 247 PHE 0.024 0.001 PHE A 49 TYR 0.011 0.001 TYR A 161 ARG 0.003 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 254) hydrogen bonds : angle 3.48286 ( 744) SS BOND : bond 0.00247 ( 17) SS BOND : angle 1.67996 ( 34) covalent geometry : bond 0.00388 ( 4747) covalent geometry : angle 0.52525 ( 6393) *********************** 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 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.1579 time to fit residues: 10.2726 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 : 0.556 ------------------------------------------------------------------------------- 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 437 CYS 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 501 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.181624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133040 restraints weight = 4955.724| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.30 r_work: 0.2982 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2403 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= 0.118 Angle : 0.509 6.729 6427 Z= 0.264 Chirality : 0.038 0.162 707 Planarity : 0.004 0.053 832 Dihedral : 5.939 57.159 641 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 1.38 % Allowed : 15.72 % 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 (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: 0.44 (0.37), residues: 580 helix: 1.08 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.60 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 214 HIS 0.004 0.001 HIS A 247 PHE 0.013 0.001 PHE A 488 TYR 0.010 0.001 TYR A 161 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 254) hydrogen bonds : angle 3.35497 ( 744) SS BOND : bond 0.00241 ( 17) SS BOND : angle 1.46835 ( 34) covalent geometry : bond 0.00290 ( 4747) covalent geometry : angle 0.49861 ( 6393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 245 CYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8029 (t) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1558 time to fit residues: 10.2077 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 : 0.550 ------------------------------------------------------------------------------- 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 437 CYS 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 501 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.0030 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.183802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134669 restraints weight = 4927.641| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.42 r_work: 0.3007 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 4764 Z= 0.103 Angle : 0.486 5.919 6427 Z= 0.252 Chirality : 0.037 0.148 707 Planarity : 0.004 0.053 832 Dihedral : 5.727 56.320 641 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % Rotamer: Outliers : 1.18 % Allowed : 16.11 % 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 (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: 0.62 (0.38), residues: 580 helix: 1.25 (0.27), residues: 409 sheet: None (None), residues: 0 loop : -1.65 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 214 HIS 0.004 0.001 HIS A 247 PHE 0.012 0.001 PHE A 488 TYR 0.009 0.001 TYR A 161 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 254) hydrogen bonds : angle 3.24438 ( 744) SS BOND : bond 0.00226 ( 17) SS BOND : angle 1.29482 ( 34) covalent geometry : bond 0.00240 ( 4747) covalent geometry : angle 0.47843 ( 6393) ********************** 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 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 245 CYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8014 (t) REVERT: A 519 LYS cc_start: 0.7800 (tttp) cc_final: 0.7098 (tmtt) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.1762 time to fit residues: 10.3013 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 : 0.490 ------------------------------------------------------------------------------- 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 437 CYS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 45 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 8 optimal weight: 0.0370 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.188648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139629 restraints weight = 4922.920| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.37 r_work: 0.3010 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4764 Z= 0.093 Angle : 0.468 5.366 6427 Z= 0.243 Chirality : 0.037 0.140 707 Planarity : 0.004 0.049 832 Dihedral : 5.275 57.500 641 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.59 % Favored : 92.24 % Rotamer: Outliers : 1.77 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.38), residues: 580 helix: 1.37 (0.27), residues: 410 sheet: None (None), residues: 0 loop : -1.58 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 214 HIS 0.003 0.000 HIS A 247 PHE 0.014 0.001 PHE A 488 TYR 0.009 0.001 TYR A 161 ARG 0.002 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 254) hydrogen bonds : angle 3.12341 ( 744) SS BOND : bond 0.00220 ( 17) SS BOND : angle 1.16704 ( 34) covalent geometry : bond 0.00208 ( 4747) covalent geometry : angle 0.46184 ( 6393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.13 seconds wall clock time: 46 minutes 27.28 seconds (2787.28 seconds total)