Starting phenix.real_space_refine on Wed Jul 1 23:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfk_37494/07_2026/8wfk_37494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfk_37494/07_2026/8wfk_37494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wfk_37494/07_2026/8wfk_37494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfk_37494/07_2026/8wfk_37494.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfk_37494/07_2026/8wfk_37494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfk_37494/07_2026/8wfk_37494.cif" } resolution = 3.22 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: 7 Type Number sf(0) Gaussians S 35 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 2918 2.51 5 N 683 2.21 5 O 728 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4371 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4341 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 25, 'TRANS': 520} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Unusual residues: {'W5O': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Time building chain proxies: 0.99, per 1000 atoms: 0.23 Number of scatterers: 4371 At special positions: 0 Unit cell: (84.15, 73.1, 86.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 35 16.00 Na 2 11.00 F 3 9.00 O 728 8.00 N 683 7.00 C 2918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 239 " distance=1.13 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=1.09 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: 0.41 Conformation dependent library (CDL) restraints added in 149.8 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 70.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.547A pdb=" N PHE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.928A pdb=" N ASN A 68 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 69 " --> pdb=" O LEU A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.885A pdb=" N ILE A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.068A pdb=" N ALA A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.800A pdb=" N VAL A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.034A pdb=" N TYR A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.544A pdb=" N CYS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.525A pdb=" N VAL A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.539A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 303 through 318 removed outlier: 4.072A pdb=" N TRP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.800A pdb=" N SER A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 371 removed outlier: 4.165A pdb=" N TYR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.631A pdb=" N THR A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.820A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.768A pdb=" N LYS A 442 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 456 removed outlier: 3.548A pdb=" N ALA A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 Proline residue: A 460 - end of helix removed outlier: 3.512A pdb=" N SER A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 463' Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.510A pdb=" N LEU A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 495 removed outlier: 4.657A pdb=" N PHE A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.840A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.623A pdb=" N ALA A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.838A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 546 207 hydrogen bonds defined for protein. 612 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: 0.58 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 637 1.31 - 1.44: 1397 1.44 - 1.56: 2421 1.56 - 1.69: 0 1.69 - 1.82: 54 Bond restraints: 4509 Sorted by residual: bond pdb=" C15 W5O A 701 " pdb=" N14 W5O A 701 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C18 W5O A 701 " pdb="CL27 W5O A 701 " ideal model delta sigma weight residual 1.727 1.784 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" C PRO A 296 " pdb=" O PRO A 296 " ideal model delta sigma weight residual 1.233 1.205 0.028 1.06e-02 8.90e+03 6.89e+00 bond pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.35e-02 5.49e+03 4.89e+00 bond pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta sigma weight residual 1.470 1.443 0.027 1.23e-02 6.61e+03 4.86e+00 ... (remaining 4504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 5940 1.45 - 2.89: 158 2.89 - 4.34: 34 4.34 - 5.78: 16 5.78 - 7.23: 2 Bond angle restraints: 6150 Sorted by residual: angle pdb=" N PRO A 296 " pdb=" CA PRO A 296 " pdb=" C PRO A 296 " ideal model delta sigma weight residual 110.55 117.00 -6.45 1.63e+00 3.76e-01 1.57e+01 angle pdb=" CA CYS A 147 " pdb=" C CYS A 147 " pdb=" N ILE A 148 " ideal model delta sigma weight residual 117.17 121.08 -3.91 1.18e+00 7.18e-01 1.10e+01 angle pdb=" CA CYS A 147 " pdb=" C CYS A 147 " pdb=" O CYS A 147 " ideal model delta sigma weight residual 120.70 117.40 3.30 1.03e+00 9.43e-01 1.03e+01 angle pdb=" CA CYS A 239 " pdb=" C CYS A 239 " pdb=" O CYS A 239 " ideal model delta sigma weight residual 120.55 117.22 3.33 1.06e+00 8.90e-01 9.88e+00 angle pdb=" N CYS A 239 " pdb=" CA CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sigma weight residual 110.12 114.69 -4.57 1.47e+00 4.63e-01 9.66e+00 ... (remaining 6145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2190 17.64 - 35.28: 283 35.28 - 52.92: 66 52.92 - 70.55: 13 70.55 - 88.19: 7 Dihedral angle restraints: 2559 sinusoidal: 987 harmonic: 1572 Sorted by residual: dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 6.64 86.36 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual 93.00 159.25 -66.25 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CA TRP A 322 " pdb=" C TRP A 322 " pdb=" N GLY A 323 " pdb=" CA GLY A 323 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 2556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 520 0.047 - 0.093: 132 0.093 - 0.139: 20 0.139 - 0.186: 2 0.186 - 0.232: 2 Chirality restraints: 676 Sorted by residual: chirality pdb=" C07 W5O A 701 " pdb=" C05 W5O A 701 " pdb=" C08 W5O A 701 " pdb=" N14 W5O A 701 " both_signs ideal model delta sigma weight residual False -2.35 -2.58 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA CYS A 147 " pdb=" N CYS A 147 " pdb=" C CYS A 147 " pdb=" CB CYS A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 673 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 209 " 0.040 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 210 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 146 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.77e+00 pdb=" C ILE A 146 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 146 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 238 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C GLY A 238 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY A 238 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 239 " -0.011 2.00e-02 2.50e+03 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 82 2.69 - 3.24: 4060 3.24 - 3.79: 6402 3.79 - 4.35: 8450 4.35 - 4.90: 14419 Nonbonded interactions: 33413 Sorted by model distance: nonbonded pdb=" O VAL A 64 " pdb="NA NA A 704 " model vdw 2.137 3.210 nonbonded pdb=" OH TYR A 316 " pdb=" O SER A 479 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR A 172 " pdb=" OE2 GLU A 213 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 414 " pdb="NA NA A 704 " model vdw 2.297 3.210 nonbonded pdb=" O TYR A 218 " pdb=" NH1 ARG A 233 " model vdw 2.312 3.120 ... (remaining 33408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.410 Find NCS groups from input model: 0.010 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.020 0.945 4511 Z= 0.989 Angle : 1.282 62.837 6154 Z= 0.634 Chirality : 0.041 0.232 676 Planarity : 0.005 0.059 753 Dihedral : 16.764 88.191 1559 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 26.90 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.97 (0.35), residues: 542 helix: -0.85 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 119 TYR 0.016 0.001 TYR A 77 PHE 0.014 0.001 PHE A 366 TRP 0.010 0.001 TRP A 554 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 ( 4509) covalent geometry : angle 0.62360 / 0.34 ( 6150) SS BOND : bond 0.92245 / 46.18 ( 2) SS BOND : angle 43.91987 / 19.02 ( 4) hydrogen bonds : bond 0.23711 / 16.40 ( 207) hydrogen bonds : angle 7.53663 / 5.48 ( 612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8355 (mttt) cc_final: 0.7203 (tttt) REVERT: A 367 MET cc_start: 0.7052 (tpt) cc_final: 0.6670 (tpt) REVERT: A 452 VAL cc_start: 0.8345 (p) cc_final: 0.8096 (t) REVERT: A 475 ASN cc_start: 0.8647 (m-40) cc_final: 0.8325 (t0) REVERT: A 531 PHE cc_start: 0.7916 (t80) cc_final: 0.7625 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0610 time to fit residues: 5.5780 Evaluate side-chains 61 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117982 restraints weight = 5694.947| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.00 r_work: 0.3258 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4511 Z= 0.130 Angle : 0.584 7.189 6154 Z= 0.298 Chirality : 0.041 0.112 676 Planarity : 0.005 0.051 753 Dihedral : 5.345 46.857 625 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.04 % Allowed : 26.03 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.35 (0.36), residues: 542 helix: -0.23 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -2.15 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.014 0.001 TYR A 141 PHE 0.010 0.001 PHE A 366 TRP 0.012 0.001 TRP A 554 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 4509) covalent geometry : angle 0.57904 / 0.30 ( 6150) SS BOND : bond 0.00444 / 0.21 ( 2) SS BOND : angle 3.06298 / 1.19 ( 4) hydrogen bonds : bond 0.05647 / 3.71 ( 207) hydrogen bonds : angle 4.79847 / 3.50 ( 612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.094 Fit side-chains REVERT: A 165 TYR cc_start: 0.8649 (m-80) cc_final: 0.8394 (m-80) REVERT: A 350 CYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 399 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.7133 (mt) REVERT: A 452 VAL cc_start: 0.8268 (p) cc_final: 0.7932 (t) REVERT: A 475 ASN cc_start: 0.8789 (m-40) cc_final: 0.8366 (t0) REVERT: A 531 PHE cc_start: 0.8233 (t80) cc_final: 0.7965 (t80) outliers start: 14 outliers final: 3 residues processed: 71 average time/residue: 0.0479 time to fit residues: 4.6139 Evaluate side-chains 63 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 399 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 52 optimal weight: 0.0470 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119648 restraints weight = 5578.792| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.88 r_work: 0.3274 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4511 Z= 0.105 Angle : 0.558 13.360 6154 Z= 0.278 Chirality : 0.039 0.112 676 Planarity : 0.005 0.047 753 Dihedral : 4.790 39.965 625 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.17 % Allowed : 25.60 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.90 (0.36), residues: 542 helix: 0.17 (0.29), residues: 361 sheet: None (None), residues: 0 loop : -2.10 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.013 0.001 TYR A 77 PHE 0.009 0.001 PHE A 366 TRP 0.012 0.001 TRP A 554 HIS 0.004 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 4509) covalent geometry : angle 0.54187 / 0.27 ( 6150) SS BOND : bond 0.00999 / 0.51 ( 2) SS BOND : angle 5.19154 / 2.39 ( 4) hydrogen bonds : bond 0.04260 / 2.79 ( 207) hydrogen bonds : angle 4.22805 / 3.10 ( 612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.151 Fit side-chains REVERT: A 399 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7129 (mt) REVERT: A 475 ASN cc_start: 0.8727 (m-40) cc_final: 0.8259 (t0) REVERT: A 531 PHE cc_start: 0.8226 (t80) cc_final: 0.7908 (t80) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.0484 time to fit residues: 4.2157 Evaluate side-chains 60 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114620 restraints weight = 5468.135| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.84 r_work: 0.3221 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4511 Z= 0.140 Angle : 0.571 9.821 6154 Z= 0.286 Chirality : 0.041 0.123 676 Planarity : 0.005 0.048 753 Dihedral : 4.644 34.918 625 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.12 % Allowed : 25.60 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.83 (0.36), residues: 542 helix: 0.23 (0.29), residues: 362 sheet: None (None), residues: 0 loop : -2.12 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.016 0.001 TYR A 141 PHE 0.009 0.001 PHE A 361 TRP 0.012 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 4509) covalent geometry : angle 0.55638 / 0.28 ( 6150) SS BOND : bond 0.00492 / 0.25 ( 2) SS BOND : angle 4.98299 / 2.31 ( 4) hydrogen bonds : bond 0.04762 / 3.08 ( 207) hydrogen bonds : angle 4.12089 / 3.02 ( 612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.162 Fit side-chains REVERT: A 174 ASP cc_start: 0.6529 (m-30) cc_final: 0.6212 (t0) REVERT: A 399 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7236 (mt) REVERT: A 475 ASN cc_start: 0.8751 (m-40) cc_final: 0.8268 (t0) REVERT: A 531 PHE cc_start: 0.8306 (t80) cc_final: 0.7986 (t80) outliers start: 19 outliers final: 8 residues processed: 67 average time/residue: 0.0556 time to fit residues: 5.1137 Evaluate side-chains 63 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112665 restraints weight = 5727.597| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.03 r_work: 0.3148 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 4511 Z= 0.188 Angle : 0.615 6.676 6154 Z= 0.313 Chirality : 0.043 0.131 676 Planarity : 0.005 0.043 753 Dihedral : 4.775 32.170 625 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.90 % Allowed : 25.38 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.98 (0.36), residues: 542 helix: -0.02 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.019 0.001 TYR A 141 PHE 0.012 0.001 PHE A 361 TRP 0.015 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 ( 4509) covalent geometry : angle 0.60233 / 0.31 ( 6150) SS BOND : bond 0.00802 / 0.42 ( 2) SS BOND : angle 5.00045 / 2.46 ( 4) hydrogen bonds : bond 0.05564 / 3.58 ( 207) hydrogen bonds : angle 4.18073 / 3.04 ( 612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.145 Fit side-chains REVERT: A 174 ASP cc_start: 0.6478 (m-30) cc_final: 0.6183 (t0) REVERT: A 399 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7242 (mt) REVERT: A 531 PHE cc_start: 0.8204 (t80) cc_final: 0.7921 (t80) outliers start: 18 outliers final: 11 residues processed: 67 average time/residue: 0.0524 time to fit residues: 4.7898 Evaluate side-chains 67 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114425 restraints weight = 5696.654| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.87 r_work: 0.3213 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4511 Z= 0.110 Angle : 0.532 6.449 6154 Z= 0.267 Chirality : 0.040 0.115 676 Planarity : 0.005 0.043 753 Dihedral : 4.546 30.852 625 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.47 % Allowed : 26.03 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.63 (0.37), residues: 542 helix: 0.38 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -1.99 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.013 0.001 TYR A 77 PHE 0.008 0.001 PHE A 358 TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 4509) covalent geometry : angle 0.52456 / 0.26 ( 6150) SS BOND : bond 0.00615 / 0.32 ( 2) SS BOND : angle 3.41593 / 1.66 ( 4) hydrogen bonds : bond 0.04195 / 2.70 ( 207) hydrogen bonds : angle 3.92864 / 2.87 ( 612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.157 Fit side-chains REVERT: A 104 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 174 ASP cc_start: 0.6544 (m-30) cc_final: 0.6211 (t0) REVERT: A 399 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7226 (mt) REVERT: A 531 PHE cc_start: 0.8371 (t80) cc_final: 0.8077 (t80) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.0560 time to fit residues: 5.1281 Evaluate side-chains 66 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.0470 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115685 restraints weight = 5601.659| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.92 r_work: 0.3224 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 4511 Z= 0.108 Angle : 0.547 7.502 6154 Z= 0.275 Chirality : 0.040 0.118 676 Planarity : 0.005 0.043 753 Dihedral : 4.446 29.965 625 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.25 % Allowed : 26.25 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.42 (0.37), residues: 542 helix: 0.55 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.016 0.001 TYR A 77 PHE 0.008 0.001 PHE A 229 TRP 0.010 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4509) covalent geometry : angle 0.52555 / 0.27 ( 6150) SS BOND : bond 0.00684 / 0.35 ( 2) SS BOND : angle 5.92947 / 2.85 ( 4) hydrogen bonds : bond 0.03871 / 2.49 ( 207) hydrogen bonds : angle 3.78687 / 2.77 ( 612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.149 Fit side-chains REVERT: A 104 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 399 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7286 (mt) REVERT: A 475 ASN cc_start: 0.8743 (m-40) cc_final: 0.8293 (t0) REVERT: A 531 PHE cc_start: 0.8353 (t80) cc_final: 0.8066 (t80) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.0579 time to fit residues: 4.8202 Evaluate side-chains 64 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114949 restraints weight = 5600.907| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.90 r_work: 0.3217 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4511 Z= 0.113 Angle : 0.528 6.066 6154 Z= 0.264 Chirality : 0.040 0.117 676 Planarity : 0.005 0.043 753 Dihedral : 4.337 29.080 625 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.47 % Allowed : 26.03 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.37), residues: 542 helix: 0.66 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.00 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.016 0.001 TYR A 77 PHE 0.009 0.001 PHE A 229 TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 4509) covalent geometry : angle 0.51875 / 0.26 ( 6150) SS BOND : bond 0.00527 / 0.27 ( 2) SS BOND : angle 3.83937 / 1.94 ( 4) hydrogen bonds : bond 0.03959 / 2.56 ( 207) hydrogen bonds : angle 3.76136 / 2.75 ( 612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.107 Fit side-chains REVERT: A 104 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7995 (mp) REVERT: A 399 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7338 (mt) REVERT: A 436 ASN cc_start: 0.6779 (m110) cc_final: 0.6480 (m110) REVERT: A 475 ASN cc_start: 0.8730 (m-40) cc_final: 0.8275 (t0) REVERT: A 531 PHE cc_start: 0.8357 (t80) cc_final: 0.8067 (t80) outliers start: 16 outliers final: 14 residues processed: 63 average time/residue: 0.0551 time to fit residues: 4.7714 Evaluate side-chains 70 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112047 restraints weight = 5702.958| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.87 r_work: 0.3179 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 4511 Z= 0.170 Angle : 0.586 6.451 6154 Z= 0.294 Chirality : 0.043 0.126 676 Planarity : 0.005 0.042 753 Dihedral : 4.533 28.691 625 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.56 % Allowed : 25.16 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.52 (0.37), residues: 542 helix: 0.37 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -1.88 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.017 0.001 TYR A 141 PHE 0.011 0.001 PHE A 150 TRP 0.015 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.17 ( 4509) covalent geometry : angle 0.57861 / 0.29 ( 6150) SS BOND : bond 0.00570 / 0.30 ( 2) SS BOND : angle 3.61587 / 1.87 ( 4) hydrogen bonds : bond 0.05042 / 3.24 ( 207) hydrogen bonds : angle 3.96100 / 2.88 ( 612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.154 Fit side-chains REVERT: A 104 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 399 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7392 (mt) outliers start: 21 outliers final: 16 residues processed: 66 average time/residue: 0.0544 time to fit residues: 4.9544 Evaluate side-chains 69 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113890 restraints weight = 5691.418| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.78 r_work: 0.3222 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4511 Z= 0.112 Angle : 0.546 7.537 6154 Z= 0.274 Chirality : 0.040 0.119 676 Planarity : 0.004 0.042 753 Dihedral : 4.420 28.153 625 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.90 % Allowed : 26.46 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.29 (0.37), residues: 542 helix: 0.68 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.03 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 233 TYR 0.018 0.001 TYR A 77 PHE 0.011 0.001 PHE A 229 TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 4509) covalent geometry : angle 0.53723 / 0.27 ( 6150) SS BOND : bond 0.00654 / 0.33 ( 2) SS BOND : angle 3.94465 / 1.74 ( 4) hydrogen bonds : bond 0.03890 / 2.51 ( 207) hydrogen bonds : angle 3.75442 / 2.73 ( 612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.186 Fit side-chains REVERT: A 104 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7995 (mp) REVERT: A 399 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7394 (mt) outliers start: 18 outliers final: 12 residues processed: 62 average time/residue: 0.0569 time to fit residues: 4.8752 Evaluate side-chains 65 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 548 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115258 restraints weight = 5686.892| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.87 r_work: 0.3223 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 4511 Z= 0.127 Angle : 0.575 11.459 6154 Z= 0.289 Chirality : 0.041 0.140 676 Planarity : 0.005 0.042 753 Dihedral : 4.415 27.882 625 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.25 % Allowed : 26.90 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.23 (0.37), residues: 542 helix: 0.68 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -1.91 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.017 0.001 TYR A 77 PHE 0.012 0.001 PHE A 150 TRP 0.010 0.001 TRP A 215 HIS 0.004 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4509) covalent geometry : angle 0.54960 / 0.28 ( 6150) SS BOND : bond 0.00511 / 0.26 ( 2) SS BOND : angle 6.62746 / 3.37 ( 4) hydrogen bonds : bond 0.04148 / 2.67 ( 207) hydrogen bonds : angle 3.72202 / 2.71 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.45 seconds wall clock time: 20 minutes 2.94 seconds (1202.94 seconds total)