Starting phenix.real_space_refine on Fri Aug 22 14:47:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtu_37842/08_2025/8wtu_37842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtu_37842/08_2025/8wtu_37842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wtu_37842/08_2025/8wtu_37842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtu_37842/08_2025/8wtu_37842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wtu_37842/08_2025/8wtu_37842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtu_37842/08_2025/8wtu_37842.map" } resolution = 2.7 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= -0.001 sd= 0.069 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 20 5.16 5 C 2918 2.51 5 N 673 2.21 5 O 737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4348 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4334 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 522} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.16, per 1000 atoms: 0.27 Number of scatterers: 4348 At special positions: 0 Unit cell: (75.65, 67.15, 91.8, 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 20 16.00 O 737 8.00 N 673 7.00 C 2918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 184 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 161.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 76.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.827A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 121 Proline residue: A 108 - end of helix removed outlier: 3.582A pdb=" N GLY A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 165 removed outlier: 3.889A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.512A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.544A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.607A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.896A pdb=" N ALA A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 4.161A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.805A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 4.633A pdb=" N ALA A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.624A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 441 through 458 removed outlier: 3.659A pdb=" N PHE A 445 " --> pdb=" O HIS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.916A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 4.045A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 removed outlier: 3.634A pdb=" N LEU A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.599A pdb=" N ILE A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.527A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.630A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.572A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.623A pdb=" N GLY A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.810A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.575A pdb=" N PHE A 609 " --> pdb=" O ILE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.923A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 250 hydrogen bonds defined for protein. 723 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: 0.67 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1264 1.34 - 1.46: 1123 1.46 - 1.58: 2071 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4489 Sorted by residual: bond pdb=" C PHE A 82 " pdb=" N PRO A 83 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.51e-02 4.39e+03 2.93e+00 bond pdb=" CB PRO A 285 " pdb=" CG PRO A 285 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.72e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 1.521 1.532 -0.011 1.14e-02 7.69e+03 8.98e-01 ... (remaining 4484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6011 2.00 - 3.99: 99 3.99 - 5.99: 15 5.99 - 7.99: 0 7.99 - 9.98: 1 Bond angle restraints: 6126 Sorted by residual: angle pdb=" N VAL A 262 " pdb=" CA VAL A 262 " pdb=" C VAL A 262 " ideal model delta sigma weight residual 106.21 111.73 -5.52 1.07e+00 8.73e-01 2.66e+01 angle pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 113.47 108.74 4.73 1.01e+00 9.80e-01 2.20e+01 angle pdb=" N ILE A 537 " pdb=" CA ILE A 537 " pdb=" C ILE A 537 " ideal model delta sigma weight residual 111.81 108.41 3.40 8.60e-01 1.35e+00 1.56e+01 angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 119.78 115.17 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 113.10 109.51 3.59 9.70e-01 1.06e+00 1.37e+01 ... (remaining 6121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 2365 21.46 - 42.92: 127 42.92 - 64.38: 11 64.38 - 85.84: 11 85.84 - 107.30: 8 Dihedral angle restraints: 2522 sinusoidal: 954 harmonic: 1568 Sorted by residual: dihedral pdb=" CB CYS A 176 " pdb=" SG CYS A 176 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual 93.00 134.08 -41.08 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA LEU A 252 " pdb=" C LEU A 252 " pdb=" N TRP A 253 " pdb=" CA TRP A 253 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual 53.78 -53.52 107.30 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 2519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 414 0.032 - 0.065: 206 0.065 - 0.097: 47 0.097 - 0.129: 18 0.129 - 0.162: 3 Chirality restraints: 688 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA TYR A 152 " pdb=" N TYR A 152 " pdb=" C TYR A 152 " pdb=" CB TYR A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA PRO A 513 " pdb=" N PRO A 513 " pdb=" C PRO A 513 " pdb=" CB PRO A 513 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 685 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ILE A 103 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 103 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 104 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 253 " -0.013 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP A 253 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 253 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 253 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 253 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 253 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 253 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 253 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 253 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 253 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 512 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A 513 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " -0.028 5.00e-02 4.00e+02 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1259 2.82 - 3.34: 3972 3.34 - 3.86: 6955 3.86 - 4.38: 8045 4.38 - 4.90: 14339 Nonbonded interactions: 34570 Sorted by model distance: nonbonded pdb=" OG SER A 182 " pdb=" OE2 GLU A 212 " model vdw 2.301 3.040 nonbonded pdb=" NE2 HIS A 280 " pdb=" OG1 THR A 397 " model vdw 2.305 3.120 nonbonded pdb=" NZ LYS A 522 " pdb=" O ALA A 616 " model vdw 2.321 3.120 nonbonded pdb=" O ILE A 561 " pdb=" OG SER A 564 " model vdw 2.388 3.040 nonbonded pdb=" O PHE A 72 " pdb=" OH TYR A 271 " model vdw 2.443 3.040 ... (remaining 34565 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: 2.810 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.550 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4491 Z= 0.145 Angle : 0.679 9.984 6131 Z= 0.441 Chirality : 0.041 0.162 688 Planarity : 0.005 0.052 743 Dihedral : 15.115 107.297 1521 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 aren not related in a simple way. whole: 0.10 (0.38), residues: 538 helix: 0.95 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -1.67 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.030 0.001 TYR A 152 PHE 0.014 0.001 PHE A 335 TRP 0.034 0.001 TRP A 253 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4489) covalent geometry : angle 0.67837 ( 6126) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.26614 ( 2) hydrogen bonds : bond 0.14948 ( 250) hydrogen bonds : angle 5.46410 ( 723) link_NAG-ASN : bond 0.00122 ( 1) link_NAG-ASN : angle 0.69331 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.102 Fit side-chains REVERT: A 75 ASP cc_start: 0.7204 (t70) cc_final: 0.6959 (t70) REVERT: A 206 LYS cc_start: 0.7607 (ptpt) cc_final: 0.7118 (ptmt) REVERT: A 329 PHE cc_start: 0.7352 (m-80) cc_final: 0.6679 (t80) REVERT: A 375 ASN cc_start: 0.7708 (m-40) cc_final: 0.7238 (m110) REVERT: A 528 PHE cc_start: 0.6736 (m-10) cc_final: 0.6427 (m-80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4765 time to fit residues: 44.5041 Evaluate side-chains 51 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 289 ASN A 292 ASN A 350 ASN A 507 GLN A 555 ASN A 596 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.125701 restraints weight = 4506.430| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 0.76 r_work: 0.3124 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4491 Z= 0.138 Angle : 0.571 7.029 6131 Z= 0.294 Chirality : 0.042 0.166 688 Planarity : 0.005 0.050 743 Dihedral : 6.527 46.881 605 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.53 % Allowed : 8.97 % Favored : 89.50 % 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 aren not related in a simple way. whole: 0.57 (0.38), residues: 538 helix: 1.29 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -1.42 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.024 0.002 TYR A 111 PHE 0.015 0.001 PHE A 94 TRP 0.020 0.001 TRP A 253 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4489) covalent geometry : angle 0.56938 ( 6126) SS BOND : bond 0.00818 ( 1) SS BOND : angle 2.71592 ( 2) hydrogen bonds : bond 0.06688 ( 250) hydrogen bonds : angle 4.47836 ( 723) link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 0.64744 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.262 Fit side-chains REVERT: A 206 LYS cc_start: 0.7938 (ptpt) cc_final: 0.7433 (ptmt) REVERT: A 329 PHE cc_start: 0.8021 (m-80) cc_final: 0.7477 (t80) REVERT: A 375 ASN cc_start: 0.8047 (m-40) cc_final: 0.7686 (m110) REVERT: A 381 THR cc_start: 0.8030 (p) cc_final: 0.7732 (t) REVERT: A 436 GLN cc_start: 0.7905 (mm110) cc_final: 0.7612 (mp-120) REVERT: A 586 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7776 (mt-10) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 0.4411 time to fit residues: 25.3587 Evaluate side-chains 52 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.136955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.124618 restraints weight = 4492.845| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.77 r_work: 0.3120 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4491 Z= 0.127 Angle : 0.525 6.233 6131 Z= 0.276 Chirality : 0.040 0.132 688 Planarity : 0.005 0.049 743 Dihedral : 4.492 27.735 605 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.19 % Allowed : 9.19 % Favored : 88.62 % 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 aren not related in a simple way. whole: 0.79 (0.38), residues: 538 helix: 1.55 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.43 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.017 0.002 TYR A 84 PHE 0.013 0.001 PHE A 409 TRP 0.013 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4489) covalent geometry : angle 0.52238 ( 6126) SS BOND : bond 0.00537 ( 1) SS BOND : angle 2.38420 ( 2) hydrogen bonds : bond 0.06330 ( 250) hydrogen bonds : angle 4.39677 ( 723) link_NAG-ASN : bond 0.00381 ( 1) link_NAG-ASN : angle 1.32307 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.110 Fit side-chains REVERT: A 206 LYS cc_start: 0.7902 (ptpt) cc_final: 0.7316 (pttt) REVERT: A 271 TYR cc_start: 0.8388 (m-80) cc_final: 0.8181 (m-80) REVERT: A 329 PHE cc_start: 0.7979 (m-80) cc_final: 0.7482 (t80) REVERT: A 375 ASN cc_start: 0.8052 (m-40) cc_final: 0.7692 (m110) REVERT: A 381 THR cc_start: 0.7987 (p) cc_final: 0.7741 (t) REVERT: A 436 GLN cc_start: 0.7881 (mm110) cc_final: 0.7604 (mp-120) REVERT: A 586 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7614 (mt-10) outliers start: 10 outliers final: 3 residues processed: 54 average time/residue: 0.4793 time to fit residues: 26.8807 Evaluate side-chains 51 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.129598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116450 restraints weight = 4428.268| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 0.81 r_work: 0.3025 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4491 Z= 0.186 Angle : 0.631 6.778 6131 Z= 0.334 Chirality : 0.044 0.145 688 Planarity : 0.006 0.056 743 Dihedral : 4.761 25.910 605 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.84 % Allowed : 10.28 % Favored : 86.87 % 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 aren not related in a simple way. whole: 0.59 (0.37), residues: 538 helix: 1.30 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.34 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 587 TYR 0.020 0.002 TYR A 111 PHE 0.022 0.002 PHE A 409 TRP 0.011 0.002 TRP A 553 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4489) covalent geometry : angle 0.62728 ( 6126) SS BOND : bond 0.00840 ( 1) SS BOND : angle 3.55426 ( 2) hydrogen bonds : bond 0.08569 ( 250) hydrogen bonds : angle 4.67816 ( 723) link_NAG-ASN : bond 0.00252 ( 1) link_NAG-ASN : angle 1.45446 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.161 Fit side-chains REVERT: A 206 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7476 (ptmt) REVERT: A 329 PHE cc_start: 0.7992 (m-80) cc_final: 0.7460 (t80) REVERT: A 375 ASN cc_start: 0.8185 (m-40) cc_final: 0.7751 (m110) REVERT: A 377 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 381 THR cc_start: 0.8152 (p) cc_final: 0.7895 (t) REVERT: A 436 GLN cc_start: 0.7862 (mm110) cc_final: 0.7540 (mp-120) REVERT: A 541 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7410 (mptt) REVERT: A 586 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7728 (mt-10) outliers start: 13 outliers final: 4 residues processed: 54 average time/residue: 0.4598 time to fit residues: 25.8778 Evaluate side-chains 53 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.134715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.122074 restraints weight = 4500.979| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.82 r_work: 0.3102 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4491 Z= 0.129 Angle : 0.524 5.812 6131 Z= 0.278 Chirality : 0.040 0.128 688 Planarity : 0.005 0.056 743 Dihedral : 4.584 35.424 605 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 10.72 % Favored : 86.43 % 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 aren not related in a simple way. whole: 0.98 (0.38), residues: 538 helix: 1.64 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.29 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 409 TRP 0.014 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4489) covalent geometry : angle 0.51523 ( 6126) SS BOND : bond 0.00377 ( 1) SS BOND : angle 2.76666 ( 2) hydrogen bonds : bond 0.06491 ( 250) hydrogen bonds : angle 4.44069 ( 723) link_NAG-ASN : bond 0.00562 ( 1) link_NAG-ASN : angle 3.67258 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.153 Fit side-chains REVERT: A 206 LYS cc_start: 0.7924 (ptpt) cc_final: 0.7391 (pttp) REVERT: A 329 PHE cc_start: 0.8023 (m-80) cc_final: 0.7522 (t80) REVERT: A 375 ASN cc_start: 0.8108 (m-40) cc_final: 0.7683 (m110) REVERT: A 377 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 436 GLN cc_start: 0.7953 (mm110) cc_final: 0.7630 (mp-120) REVERT: A 586 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7645 (mt-10) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 0.4541 time to fit residues: 26.0239 Evaluate side-chains 54 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.0050 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.137552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.125363 restraints weight = 4582.878| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.77 r_work: 0.3153 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4491 Z= 0.115 Angle : 0.491 6.098 6131 Z= 0.259 Chirality : 0.039 0.173 688 Planarity : 0.005 0.053 743 Dihedral : 4.216 28.452 605 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.41 % Allowed : 12.47 % Favored : 85.12 % 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 aren not related in a simple way. whole: 1.26 (0.38), residues: 538 helix: 1.89 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.25 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.015 0.001 TYR A 84 PHE 0.010 0.001 PHE A 409 TRP 0.014 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 4489) covalent geometry : angle 0.48488 ( 6126) SS BOND : bond 0.00461 ( 1) SS BOND : angle 2.17306 ( 2) hydrogen bonds : bond 0.05712 ( 250) hydrogen bonds : angle 4.31518 ( 723) link_NAG-ASN : bond 0.00947 ( 1) link_NAG-ASN : angle 3.08004 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.153 Fit side-chains REVERT: A 206 LYS cc_start: 0.7846 (ptpt) cc_final: 0.7334 (pttp) REVERT: A 329 PHE cc_start: 0.7983 (m-80) cc_final: 0.7555 (t80) REVERT: A 375 ASN cc_start: 0.8040 (m-40) cc_final: 0.7638 (m110) REVERT: A 377 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: A 436 GLN cc_start: 0.7885 (mm110) cc_final: 0.7498 (mp-120) REVERT: A 541 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7232 (mptt) REVERT: A 586 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7986 (mp0) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.4847 time to fit residues: 27.7395 Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.134199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121369 restraints weight = 4535.463| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.81 r_work: 0.3098 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4491 Z= 0.131 Angle : 0.525 6.620 6131 Z= 0.278 Chirality : 0.041 0.174 688 Planarity : 0.005 0.055 743 Dihedral : 4.374 29.306 605 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.63 % Allowed : 12.04 % Favored : 85.34 % 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 aren not related in a simple way. whole: 1.31 (0.38), residues: 538 helix: 1.94 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.017 0.001 TYR A 84 PHE 0.014 0.001 PHE A 409 TRP 0.013 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4489) covalent geometry : angle 0.51917 ( 6126) SS BOND : bond 0.00499 ( 1) SS BOND : angle 2.43747 ( 2) hydrogen bonds : bond 0.06566 ( 250) hydrogen bonds : angle 4.39102 ( 723) link_NAG-ASN : bond 0.00812 ( 1) link_NAG-ASN : angle 2.97060 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.151 Fit side-chains REVERT: A 206 LYS cc_start: 0.7833 (ptpt) cc_final: 0.7280 (pttp) REVERT: A 329 PHE cc_start: 0.8031 (m-80) cc_final: 0.7562 (t80) REVERT: A 375 ASN cc_start: 0.8102 (m-40) cc_final: 0.7700 (m110) REVERT: A 377 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 436 GLN cc_start: 0.7932 (mm110) cc_final: 0.7552 (mp-120) REVERT: A 541 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7351 (mptt) REVERT: A 586 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7636 (mt-10) outliers start: 12 outliers final: 9 residues processed: 51 average time/residue: 0.4540 time to fit residues: 24.1320 Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.135417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.122402 restraints weight = 4563.917| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.83 r_work: 0.3107 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4491 Z= 0.123 Angle : 0.506 6.352 6131 Z= 0.268 Chirality : 0.040 0.183 688 Planarity : 0.005 0.054 743 Dihedral : 4.254 27.669 605 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.63 % Allowed : 11.82 % Favored : 85.56 % 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 aren not related in a simple way. whole: 1.44 (0.38), residues: 538 helix: 2.09 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -1.23 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.016 0.001 TYR A 84 PHE 0.012 0.001 PHE A 409 TRP 0.013 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4489) covalent geometry : angle 0.50090 ( 6126) SS BOND : bond 0.00423 ( 1) SS BOND : angle 2.31299 ( 2) hydrogen bonds : bond 0.06138 ( 250) hydrogen bonds : angle 4.33811 ( 723) link_NAG-ASN : bond 0.00816 ( 1) link_NAG-ASN : angle 2.88042 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.112 Fit side-chains REVERT: A 206 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7266 (pttp) REVERT: A 329 PHE cc_start: 0.8022 (m-80) cc_final: 0.7559 (t80) REVERT: A 375 ASN cc_start: 0.8083 (m-40) cc_final: 0.7689 (m110) REVERT: A 377 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 436 GLN cc_start: 0.7927 (mm110) cc_final: 0.7541 (mp-120) REVERT: A 541 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7261 (mptt) REVERT: A 586 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8053 (mp0) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.4473 time to fit residues: 24.1584 Evaluate side-chains 56 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.133156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.120052 restraints weight = 4518.463| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 0.86 r_work: 0.3100 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4491 Z= 0.138 Angle : 0.534 6.753 6131 Z= 0.284 Chirality : 0.041 0.177 688 Planarity : 0.005 0.055 743 Dihedral : 4.450 28.865 605 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.06 % Allowed : 11.38 % Favored : 85.56 % 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 aren not related in a simple way. whole: 1.43 (0.38), residues: 538 helix: 2.00 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -1.01 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.017 0.001 TYR A 84 PHE 0.015 0.001 PHE A 409 TRP 0.012 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4489) covalent geometry : angle 0.52916 ( 6126) SS BOND : bond 0.00522 ( 1) SS BOND : angle 2.56411 ( 2) hydrogen bonds : bond 0.06895 ( 250) hydrogen bonds : angle 4.42872 ( 723) link_NAG-ASN : bond 0.00757 ( 1) link_NAG-ASN : angle 2.68379 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.108 Fit side-chains REVERT: A 206 LYS cc_start: 0.7908 (ptpt) cc_final: 0.7336 (pttp) REVERT: A 329 PHE cc_start: 0.8011 (m-80) cc_final: 0.7537 (t80) REVERT: A 375 ASN cc_start: 0.8094 (m-40) cc_final: 0.7679 (m110) REVERT: A 377 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: A 436 GLN cc_start: 0.7892 (mm110) cc_final: 0.7518 (mp-120) REVERT: A 506 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: A 541 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7365 (mptt) REVERT: A 586 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7627 (mt-10) outliers start: 14 outliers final: 7 residues processed: 55 average time/residue: 0.4262 time to fit residues: 24.5001 Evaluate side-chains 56 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.0060 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.134395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.121160 restraints weight = 4497.791| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.85 r_work: 0.3100 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4491 Z= 0.128 Angle : 0.517 6.395 6131 Z= 0.274 Chirality : 0.040 0.184 688 Planarity : 0.005 0.054 743 Dihedral : 4.339 27.427 605 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.41 % Allowed : 12.04 % Favored : 85.56 % 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 aren not related in a simple way. whole: 1.59 (0.38), residues: 538 helix: 2.17 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.00 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 409 TRP 0.014 0.001 TRP A 585 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4489) covalent geometry : angle 0.51194 ( 6126) SS BOND : bond 0.00451 ( 1) SS BOND : angle 2.40008 ( 2) hydrogen bonds : bond 0.06415 ( 250) hydrogen bonds : angle 4.37918 ( 723) link_NAG-ASN : bond 0.00759 ( 1) link_NAG-ASN : angle 2.61899 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.115 Fit side-chains REVERT: A 206 LYS cc_start: 0.7876 (ptpt) cc_final: 0.7297 (pttp) REVERT: A 329 PHE cc_start: 0.8017 (m-80) cc_final: 0.7536 (t80) REVERT: A 375 ASN cc_start: 0.8078 (m-40) cc_final: 0.7656 (m110) REVERT: A 377 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 436 GLN cc_start: 0.7913 (mm110) cc_final: 0.7519 (mp-120) REVERT: A 506 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 541 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7346 (mptt) REVERT: A 586 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7628 (mt-10) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.4597 time to fit residues: 24.8358 Evaluate side-chains 56 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.134472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.121665 restraints weight = 4557.111| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.85 r_work: 0.3099 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4491 Z= 0.129 Angle : 0.518 6.491 6131 Z= 0.275 Chirality : 0.040 0.185 688 Planarity : 0.005 0.054 743 Dihedral : 4.298 25.990 605 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.19 % Allowed : 12.47 % Favored : 85.34 % 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 aren not related in a simple way. whole: 1.59 (0.38), residues: 538 helix: 2.18 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.00 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 409 TRP 0.015 0.001 TRP A 585 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4489) covalent geometry : angle 0.51345 ( 6126) SS BOND : bond 0.00441 ( 1) SS BOND : angle 2.40546 ( 2) hydrogen bonds : bond 0.06428 ( 250) hydrogen bonds : angle 4.37747 ( 723) link_NAG-ASN : bond 0.00743 ( 1) link_NAG-ASN : angle 2.46318 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1372.94 seconds wall clock time: 24 minutes 3.59 seconds (1443.59 seconds total)