Starting phenix.real_space_refine on Sat May 2 09:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkh_61561/05_2026/9jkh_61561.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkh_61561/05_2026/9jkh_61561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jkh_61561/05_2026/9jkh_61561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkh_61561/05_2026/9jkh_61561.map" model { file = "/net/cci-nas-00/data/ceres_data/9jkh_61561/05_2026/9jkh_61561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkh_61561/05_2026/9jkh_61561.cif" } resolution = 3.2 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= -0.002 sd= 0.091 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 23 5.16 5 C 2789 2.51 5 N 658 2.21 5 O 709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4179 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4178 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 23, 'TRANS': 505} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.27, per 1000 atoms: 0.30 Number of scatterers: 4179 At special positions: 0 Unit cell: (73.6912, 65.3172, 88.7644, 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 23 16.00 O 709 8.00 N 658 7.00 C 2789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 157.2 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 62.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 101 through 110 removed outlier: 3.672A pdb=" N VAL A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 removed outlier: 4.608A pdb=" N MET A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.808A pdb=" N LYS A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 134 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 135 " --> pdb=" O TRP A 132 " (cutoff:3.500A) Proline residue: A 136 - end of helix No H-bonds generated for 'chain 'A' and resid 130 through 138' Processing helix chain 'A' and resid 139 through 168 removed outlier: 3.712A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.525A pdb=" N TYR A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.559A pdb=" N GLN A 226 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 227 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 272 through 287 removed outlier: 4.109A pdb=" N THR A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.890A pdb=" N ARG A 295 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 296 " --> pdb=" O GLY A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.719A pdb=" N ASP A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.965A pdb=" N TYR A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 375 removed outlier: 3.563A pdb=" N VAL A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 389 through 399 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 425 removed outlier: 3.720A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.693A pdb=" N ASP A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.744A pdb=" N HIS A 442 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 443 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 443' Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.673A pdb=" N LEU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 481 through 493 removed outlier: 3.673A pdb=" N LEU A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 513 removed outlier: 4.323A pdb=" N ASP A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 532 through 542 removed outlier: 3.662A pdb=" N ILE A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 560 Processing helix chain 'A' and resid 564 through 568 removed outlier: 4.108A pdb=" N SER A 567 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 579 removed outlier: 4.969A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 171 hydrogen bonds defined for protein. 501 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: 0.52 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1238 1.34 - 1.46: 1086 1.46 - 1.58: 1950 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 4308 Sorted by residual: bond pdb=" C PHE A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 1.333 1.406 -0.072 1.44e-02 4.82e+03 2.52e+01 bond pdb=" CB ASN A 181 " pdb=" CG ASN A 181 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.03e+00 bond pdb=" CB PRO A 101 " pdb=" CG PRO A 101 " ideal model delta sigma weight residual 1.492 1.397 0.095 5.00e-02 4.00e+02 3.57e+00 bond pdb=" C MET A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.48e+00 bond pdb=" C VAL A 572 " pdb=" N PRO A 573 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.41e+00 ... (remaining 4303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 5768 3.15 - 6.29: 91 6.29 - 9.44: 15 9.44 - 12.58: 5 12.58 - 15.73: 2 Bond angle restraints: 5881 Sorted by residual: angle pdb=" N VAL A 563 " pdb=" CA VAL A 563 " pdb=" C VAL A 563 " ideal model delta sigma weight residual 112.96 105.52 7.44 1.00e+00 1.00e+00 5.54e+01 angle pdb=" N ILE A 268 " pdb=" CA ILE A 268 " pdb=" C ILE A 268 " ideal model delta sigma weight residual 113.71 107.20 6.51 9.50e-01 1.11e+00 4.70e+01 angle pdb=" N VAL A 83 " pdb=" CA VAL A 83 " pdb=" C VAL A 83 " ideal model delta sigma weight residual 111.88 106.48 5.40 1.06e+00 8.90e-01 2.60e+01 angle pdb=" CA LEU A 403 " pdb=" CB LEU A 403 " pdb=" CG LEU A 403 " ideal model delta sigma weight residual 116.30 132.03 -15.73 3.50e+00 8.16e-02 2.02e+01 angle pdb=" CA ASN A 181 " pdb=" CB ASN A 181 " pdb=" CG ASN A 181 " ideal model delta sigma weight residual 112.60 116.76 -4.16 1.00e+00 1.00e+00 1.73e+01 ... (remaining 5876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.76: 2026 8.76 - 17.52: 293 17.52 - 26.27: 71 26.27 - 35.03: 28 35.03 - 43.79: 13 Dihedral angle restraints: 2431 sinusoidal: 907 harmonic: 1524 Sorted by residual: dihedral pdb=" CA LYS A 579 " pdb=" C LYS A 579 " pdb=" N PHE A 580 " pdb=" CA PHE A 580 " ideal model delta harmonic sigma weight residual 180.00 154.44 25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA TRP A 520 " pdb=" C TRP A 520 " pdb=" N ARG A 521 " pdb=" CA ARG A 521 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 412 " pdb=" C PHE A 412 " pdb=" N ILE A 413 " pdb=" CA ILE A 413 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 2428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 498 0.058 - 0.117: 137 0.117 - 0.175: 27 0.175 - 0.233: 2 0.233 - 0.291: 3 Chirality restraints: 667 Sorted by residual: chirality pdb=" CB VAL A 100 " pdb=" CA VAL A 100 " pdb=" CG1 VAL A 100 " pdb=" CG2 VAL A 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ASN A 181 " pdb=" N ASN A 181 " pdb=" C ASN A 181 " pdb=" CB ASN A 181 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE A 248 " pdb=" CA ILE A 248 " pdb=" CG1 ILE A 248 " pdb=" CG2 ILE A 248 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 664 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 100 " -0.043 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 101 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 111 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 112 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 572 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO A 573 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 573 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 573 " -0.033 5.00e-02 4.00e+02 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1305 2.82 - 3.34: 3597 3.34 - 3.86: 6609 3.86 - 4.38: 8186 4.38 - 4.90: 13658 Nonbonded interactions: 33355 Sorted by model distance: nonbonded pdb=" O VAL A 538 " pdb=" OG1 THR A 542 " model vdw 2.295 3.040 nonbonded pdb=" NZ LYS A 525 " pdb=" O LYS A 619 " model vdw 2.317 3.120 nonbonded pdb=" NE2 GLN A 122 " pdb=" OD1 ASN A 340 " model vdw 2.323 3.120 nonbonded pdb=" NH1 ARG A 85 " pdb=" OD1 ASP A 476 " model vdw 2.344 3.120 nonbonded pdb=" ND2 ASN A 82 " pdb=" OG SER A 357 " model vdw 2.366 3.120 ... (remaining 33350 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: 1.300 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.140 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.006 0.095 4309 Z= 0.255 Angle : 1.055 15.726 5883 Z= 0.543 Chirality : 0.056 0.291 667 Planarity : 0.008 0.063 720 Dihedral : 9.921 43.789 1454 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.23 % Allowed : 5.18 % Favored : 94.59 % 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: -6.40 (0.22), residues: 523 helix: -4.63 (0.11), residues: 342 sheet: None (None), residues: 0 loop : -2.96 (0.37), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 283 TYR 0.028 0.003 TYR A 151 PHE 0.026 0.002 PHE A 155 TRP 0.022 0.003 TRP A 520 HIS 0.007 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 4308) covalent geometry : angle 1.05496 ( 5881) SS BOND : bond 0.00240 ( 1) SS BOND : angle 1.49602 ( 2) hydrogen bonds : bond 0.32778 ( 171) hydrogen bonds : angle 11.81159 ( 501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.092 Fit side-chains REVERT: A 104 LEU cc_start: 0.8746 (tm) cc_final: 0.8432 (tp) REVERT: A 491 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7537 (tt0) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0426 time to fit residues: 5.8274 Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.0020 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 157 ASN A 239 GLN A 353 ASN A 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.152162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127038 restraints weight = 5042.260| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.77 r_work: 0.3036 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4309 Z= 0.116 Angle : 0.698 11.813 5883 Z= 0.348 Chirality : 0.041 0.163 667 Planarity : 0.006 0.038 720 Dihedral : 5.816 22.444 568 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.25 % Allowed : 9.01 % Favored : 88.74 % 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: -4.18 (0.29), residues: 523 helix: -2.81 (0.21), residues: 347 sheet: None (None), residues: 0 loop : -2.26 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.013 0.001 TYR A 274 PHE 0.011 0.001 PHE A 114 TRP 0.019 0.001 TRP A 267 HIS 0.002 0.000 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4308) covalent geometry : angle 0.69756 ( 5881) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.71620 ( 2) hydrogen bonds : bond 0.04675 ( 171) hydrogen bonds : angle 5.44889 ( 501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.156 Fit side-chains REVERT: A 104 LEU cc_start: 0.8696 (tm) cc_final: 0.8315 (tp) REVERT: A 116 MET cc_start: 0.8766 (ttm) cc_final: 0.8513 (ttp) REVERT: A 336 ASN cc_start: 0.8279 (m-40) cc_final: 0.8020 (m-40) REVERT: A 424 MET cc_start: 0.8584 (ttp) cc_final: 0.8345 (ttp) REVERT: A 437 GLU cc_start: 0.8019 (tp30) cc_final: 0.7770 (mm-30) REVERT: A 491 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7778 (tt0) outliers start: 10 outliers final: 5 residues processed: 94 average time/residue: 0.0488 time to fit residues: 6.3502 Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110457 restraints weight = 5064.956| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.73 r_work: 0.2956 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4309 Z= 0.144 Angle : 0.707 13.598 5883 Z= 0.342 Chirality : 0.042 0.161 667 Planarity : 0.004 0.035 720 Dihedral : 5.524 23.749 568 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.38 % Allowed : 11.94 % Favored : 84.68 % 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: -2.77 (0.33), residues: 523 helix: -1.66 (0.25), residues: 349 sheet: None (None), residues: 0 loop : -1.86 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 283 TYR 0.018 0.001 TYR A 115 PHE 0.016 0.001 PHE A 155 TRP 0.010 0.001 TRP A 520 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4308) covalent geometry : angle 0.70702 ( 5881) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.73791 ( 2) hydrogen bonds : bond 0.04258 ( 171) hydrogen bonds : angle 4.91152 ( 501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.147 Fit side-chains REVERT: A 104 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8340 (tp) REVERT: A 252 TYR cc_start: 0.8383 (t80) cc_final: 0.8072 (t80) REVERT: A 267 TRP cc_start: 0.7556 (t-100) cc_final: 0.7160 (t60) REVERT: A 336 ASN cc_start: 0.8397 (m-40) cc_final: 0.8160 (m-40) REVERT: A 491 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7844 (tt0) REVERT: A 544 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5192 (pmt100) REVERT: A 619 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7789 (ttmt) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 0.0580 time to fit residues: 5.9568 Evaluate side-chains 73 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 619 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109802 restraints weight = 5031.704| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.73 r_work: 0.2947 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4309 Z= 0.135 Angle : 0.685 14.208 5883 Z= 0.328 Chirality : 0.041 0.161 667 Planarity : 0.004 0.038 720 Dihedral : 5.441 25.733 568 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.15 % Allowed : 13.29 % Favored : 83.56 % 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: -2.00 (0.35), residues: 523 helix: -1.06 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 283 TYR 0.010 0.001 TYR A 115 PHE 0.014 0.001 PHE A 155 TRP 0.010 0.001 TRP A 520 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4308) covalent geometry : angle 0.68468 ( 5881) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.68718 ( 2) hydrogen bonds : bond 0.03887 ( 171) hydrogen bonds : angle 4.64391 ( 501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.148 Fit side-chains REVERT: A 104 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8324 (tp) REVERT: A 252 TYR cc_start: 0.8431 (t80) cc_final: 0.8088 (t80) REVERT: A 256 TRP cc_start: 0.6441 (t60) cc_final: 0.5572 (t60) REVERT: A 437 GLU cc_start: 0.8229 (tp30) cc_final: 0.8006 (mm-30) REVERT: A 491 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7837 (tt0) REVERT: A 544 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5125 (pmt100) REVERT: A 588 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7663 (ttt180) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.0807 time to fit residues: 7.9099 Evaluate side-chains 76 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.0070 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102490 restraints weight = 5043.975| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.92 r_work: 0.2944 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4309 Z= 0.120 Angle : 0.664 15.054 5883 Z= 0.318 Chirality : 0.040 0.159 667 Planarity : 0.004 0.040 720 Dihedral : 5.280 25.176 568 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.28 % Allowed : 11.94 % Favored : 83.78 % 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: -1.49 (0.36), residues: 523 helix: -0.62 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.50 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.009 0.001 TYR A 115 PHE 0.012 0.001 PHE A 155 TRP 0.010 0.001 TRP A 520 HIS 0.002 0.000 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4308) covalent geometry : angle 0.66371 ( 5881) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.58130 ( 2) hydrogen bonds : bond 0.03624 ( 171) hydrogen bonds : angle 4.45829 ( 501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.144 Fit side-chains REVERT: A 104 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8215 (tp) REVERT: A 250 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8017 (tt) REVERT: A 252 TYR cc_start: 0.8457 (t80) cc_final: 0.8091 (t80) REVERT: A 256 TRP cc_start: 0.6401 (t60) cc_final: 0.5560 (t60) REVERT: A 424 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: A 437 GLU cc_start: 0.8212 (tp30) cc_final: 0.7997 (mm-30) REVERT: A 491 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7728 (tt0) REVERT: A 544 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.4851 (pmt100) REVERT: A 619 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7777 (ttmt) outliers start: 19 outliers final: 11 residues processed: 80 average time/residue: 0.0550 time to fit residues: 5.9394 Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 619 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.102042 restraints weight = 5138.285| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.94 r_work: 0.2938 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4309 Z= 0.119 Angle : 0.677 15.654 5883 Z= 0.321 Chirality : 0.041 0.159 667 Planarity : 0.004 0.040 720 Dihedral : 5.181 26.295 568 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.83 % Allowed : 12.16 % Favored : 84.01 % 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: -1.13 (0.37), residues: 523 helix: -0.32 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.43 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.008 0.001 TYR A 156 PHE 0.012 0.001 PHE A 155 TRP 0.009 0.001 TRP A 520 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4308) covalent geometry : angle 0.67706 ( 5881) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.45295 ( 2) hydrogen bonds : bond 0.03570 ( 171) hydrogen bonds : angle 4.37023 ( 501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.141 Fit side-chains REVERT: A 104 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8221 (tp) REVERT: A 250 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7962 (tt) REVERT: A 256 TRP cc_start: 0.6371 (t60) cc_final: 0.5601 (t60) REVERT: A 407 TRP cc_start: 0.8541 (m100) cc_final: 0.8220 (m100) REVERT: A 491 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7757 (tt0) REVERT: A 544 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5065 (pmt100) REVERT: A 619 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7813 (ttmt) outliers start: 17 outliers final: 8 residues processed: 77 average time/residue: 0.0514 time to fit residues: 5.3880 Evaluate side-chains 71 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 619 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.133696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107149 restraints weight = 5092.775| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.75 r_work: 0.2939 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4309 Z= 0.131 Angle : 0.690 15.873 5883 Z= 0.324 Chirality : 0.041 0.145 667 Planarity : 0.004 0.041 720 Dihedral : 5.201 26.227 568 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.38 % Allowed : 13.06 % Favored : 83.56 % 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: -0.89 (0.37), residues: 523 helix: -0.12 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.37 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.018 0.001 TYR A 252 PHE 0.014 0.001 PHE A 155 TRP 0.008 0.001 TRP A 520 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4308) covalent geometry : angle 0.68978 ( 5881) SS BOND : bond 0.00383 ( 1) SS BOND : angle 0.66278 ( 2) hydrogen bonds : bond 0.03629 ( 171) hydrogen bonds : angle 4.39143 ( 501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.137 Fit side-chains REVERT: A 104 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8290 (tp) REVERT: A 250 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 256 TRP cc_start: 0.6433 (OUTLIER) cc_final: 0.5652 (t60) REVERT: A 407 TRP cc_start: 0.8618 (m100) cc_final: 0.8332 (m100) REVERT: A 491 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7870 (tt0) REVERT: A 544 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5234 (pmt100) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.0519 time to fit residues: 5.1133 Evaluate side-chains 73 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.0270 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.3642 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.122993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.094681 restraints weight = 5042.758| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.87 r_work: 0.2829 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4309 Z= 0.196 Angle : 0.757 16.495 5883 Z= 0.363 Chirality : 0.044 0.148 667 Planarity : 0.004 0.040 720 Dihedral : 5.545 27.314 568 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.15 % Allowed : 13.96 % Favored : 82.88 % 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: -1.05 (0.37), residues: 523 helix: -0.30 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.28 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 219 TYR 0.014 0.002 TYR A 575 PHE 0.021 0.001 PHE A 155 TRP 0.011 0.001 TRP A 256 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 4308) covalent geometry : angle 0.75659 ( 5881) SS BOND : bond 0.00521 ( 1) SS BOND : angle 1.72328 ( 2) hydrogen bonds : bond 0.04203 ( 171) hydrogen bonds : angle 4.56438 ( 501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.143 Fit side-chains REVERT: A 104 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 250 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8103 (tt) REVERT: A 256 TRP cc_start: 0.6572 (OUTLIER) cc_final: 0.5352 (t60) REVERT: A 491 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7671 (tt0) REVERT: A 514 GLN cc_start: 0.8257 (pp30) cc_final: 0.7676 (pp30) REVERT: A 544 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.5086 (pmt100) REVERT: A 588 ARG cc_start: 0.7878 (ttt180) cc_final: 0.7607 (ttt180) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.0759 time to fit residues: 7.5345 Evaluate side-chains 79 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 43 optimal weight: 0.0670 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.100466 restraints weight = 5099.607| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.83 r_work: 0.2928 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4309 Z= 0.118 Angle : 0.687 16.592 5883 Z= 0.327 Chirality : 0.040 0.150 667 Planarity : 0.003 0.039 720 Dihedral : 5.277 25.968 568 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.70 % Allowed : 13.96 % Favored : 83.33 % 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: -0.67 (0.38), residues: 523 helix: 0.04 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.25 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.014 0.001 TYR A 252 PHE 0.010 0.001 PHE A 155 TRP 0.011 0.001 TRP A 520 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4308) covalent geometry : angle 0.68644 ( 5881) SS BOND : bond 0.00293 ( 1) SS BOND : angle 1.21796 ( 2) hydrogen bonds : bond 0.03467 ( 171) hydrogen bonds : angle 4.36397 ( 501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.125 Fit side-chains REVERT: A 104 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8213 (tp) REVERT: A 250 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 256 TRP cc_start: 0.6478 (OUTLIER) cc_final: 0.5160 (t60) REVERT: A 491 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7644 (tt0) REVERT: A 544 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.4953 (pmt100) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.0592 time to fit residues: 5.6587 Evaluate side-chains 74 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 544 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.0030 chunk 46 optimal weight: 0.0370 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4468 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101641 restraints weight = 5028.001| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.85 r_work: 0.2946 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4309 Z= 0.116 Angle : 0.701 17.012 5883 Z= 0.334 Chirality : 0.040 0.148 667 Planarity : 0.004 0.040 720 Dihedral : 5.193 26.333 568 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.48 % Allowed : 14.41 % Favored : 83.11 % 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: -0.50 (0.38), residues: 523 helix: 0.18 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.20 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.018 0.001 TYR A 519 PHE 0.011 0.001 PHE A 155 TRP 0.008 0.001 TRP A 520 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4308) covalent geometry : angle 0.69698 ( 5881) SS BOND : bond 0.00255 ( 1) SS BOND : angle 4.28842 ( 2) hydrogen bonds : bond 0.03403 ( 171) hydrogen bonds : angle 4.28137 ( 501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.119 Fit side-chains REVERT: A 104 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 250 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7940 (tt) REVERT: A 256 TRP cc_start: 0.6484 (OUTLIER) cc_final: 0.5152 (t60) REVERT: A 491 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7696 (tt0) REVERT: A 544 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5009 (pmt100) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.0545 time to fit residues: 5.4854 Evaluate side-chains 78 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 605 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.130448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102833 restraints weight = 5065.053| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.86 r_work: 0.2961 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4309 Z= 0.111 Angle : 0.687 17.107 5883 Z= 0.326 Chirality : 0.040 0.150 667 Planarity : 0.003 0.041 720 Dihedral : 5.090 25.754 568 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.48 % Allowed : 14.41 % Favored : 83.11 % 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: -0.36 (0.38), residues: 523 helix: 0.31 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -1.20 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.014 0.001 TYR A 252 PHE 0.011 0.001 PHE A 155 TRP 0.009 0.001 TRP A 520 HIS 0.002 0.000 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4308) covalent geometry : angle 0.68183 ( 5881) SS BOND : bond 0.00135 ( 1) SS BOND : angle 4.71755 ( 2) hydrogen bonds : bond 0.03318 ( 171) hydrogen bonds : angle 4.25548 ( 501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1149.27 seconds wall clock time: 20 minutes 21.12 seconds (1221.12 seconds total)