Starting phenix.real_space_refine on Thu Mar 6 01:41:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtu_37842/03_2025/8wtu_37842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtu_37842/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtu_37842/03_2025/8wtu_37842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtu_37842/03_2025/8wtu_37842.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtu_37842/03_2025/8wtu_37842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtu_37842/03_2025/8wtu_37842.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.61, per 1000 atoms: 0.83 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: 0.99 Conformation dependent library (CDL) restraints added in 490.9 milliseconds 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: 0.42 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: 1.15 Time building geometry restraints manager: 1.21 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: 1.420 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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 4489 Z= 0.181 Angle : 0.678 9.984 6126 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (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 TRP 0.034 0.001 TRP A 253 HIS 0.002 0.001 HIS A 222 PHE 0.014 0.001 PHE A 335 TYR 0.030 0.001 TYR A 152 ARG 0.002 0.000 ARG A 587 *********************** 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 : 0.442 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: 1.1919 time to fit residues: 111.2866 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 : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.136798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.123761 restraints weight = 4431.717| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 0.80 r_work: 0.3089 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4489 Z= 0.184 Angle : 0.579 6.774 6126 Z= 0.299 Chirality : 0.042 0.168 688 Planarity : 0.005 0.050 743 Dihedral : 6.316 45.183 605 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.53 % Allowed : 8.75 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.38), residues: 538 helix: 1.25 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -1.44 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 253 HIS 0.004 0.001 HIS A 280 PHE 0.017 0.002 PHE A 94 TYR 0.025 0.002 TYR A 111 ARG 0.002 0.000 ARG A 301 *********************** 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 60 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.504 Fit side-chains REVERT: A 206 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7480 (ptmt) REVERT: A 329 PHE cc_start: 0.8072 (m-80) cc_final: 0.7480 (t80) REVERT: A 375 ASN cc_start: 0.8078 (m-40) cc_final: 0.7719 (m110) REVERT: A 381 THR cc_start: 0.8090 (p) cc_final: 0.7734 (t) REVERT: A 436 GLN cc_start: 0.7962 (mm110) cc_final: 0.7676 (mp-120) REVERT: A 586 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7826 (mt-10) outliers start: 7 outliers final: 2 residues processed: 56 average time/residue: 1.1217 time to fit residues: 65.7111 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 : 0.456 ------------------------------------------------------------------------------- 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 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.132921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.120601 restraints weight = 4478.419| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 0.78 r_work: 0.3078 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4489 Z= 0.201 Angle : 0.578 5.979 6126 Z= 0.306 Chirality : 0.042 0.141 688 Planarity : 0.005 0.051 743 Dihedral : 4.676 27.282 605 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 8.75 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.37), residues: 538 helix: 1.34 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.005 0.001 HIS A 280 PHE 0.018 0.002 PHE A 409 TYR 0.021 0.002 TYR A 111 ARG 0.004 0.001 ARG A 587 *********************** 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 61 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.479 Fit side-chains REVERT: A 206 LYS cc_start: 0.7949 (ptpt) cc_final: 0.7350 (pttt) REVERT: A 329 PHE cc_start: 0.8001 (m-80) cc_final: 0.7506 (t80) REVERT: A 375 ASN cc_start: 0.8115 (m-40) cc_final: 0.7734 (m110) REVERT: A 381 THR cc_start: 0.8089 (p) cc_final: 0.7845 (t) REVERT: A 436 GLN cc_start: 0.7892 (mm110) cc_final: 0.7615 (mp-120) REVERT: A 541 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7326 (mptt) REVERT: A 586 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7678 (mt-10) outliers start: 13 outliers final: 2 residues processed: 55 average time/residue: 1.1096 time to fit residues: 63.7692 Evaluate side-chains 50 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 541 LYS 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 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.135424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.122930 restraints weight = 4500.827| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.77 r_work: 0.3128 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4489 Z= 0.160 Angle : 0.513 6.032 6126 Z= 0.273 Chirality : 0.040 0.122 688 Planarity : 0.005 0.051 743 Dihedral : 4.250 21.551 605 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.41 % Allowed : 10.50 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.38), residues: 538 helix: 1.63 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.34 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 301 *********************** 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 60 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.453 Fit side-chains REVERT: A 206 LYS cc_start: 0.7888 (ptpt) cc_final: 0.7303 (pttt) REVERT: A 329 PHE cc_start: 0.7995 (m-80) cc_final: 0.7540 (t80) REVERT: A 375 ASN cc_start: 0.8061 (m-40) cc_final: 0.7628 (m110) REVERT: A 377 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 436 GLN cc_start: 0.7905 (mm110) cc_final: 0.7583 (mp-120) REVERT: A 586 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7624 (mt-10) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 1.1495 time to fit residues: 63.5939 Evaluate side-chains 52 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU 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 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.133701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.120082 restraints weight = 4581.361| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.87 r_work: 0.3075 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4489 Z= 0.172 Angle : 0.528 6.339 6126 Z= 0.281 Chirality : 0.041 0.128 688 Planarity : 0.005 0.052 743 Dihedral : 4.226 21.685 605 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.63 % Allowed : 11.60 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.38), residues: 538 helix: 1.64 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.28 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 PHE 0.014 0.001 PHE A 409 TYR 0.017 0.002 TYR A 84 ARG 0.003 0.000 ARG A 301 *********************** 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 58 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.487 Fit side-chains REVERT: A 206 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7380 (pttt) REVERT: A 329 PHE cc_start: 0.8048 (m-80) cc_final: 0.7533 (t80) REVERT: A 375 ASN cc_start: 0.8135 (m-40) cc_final: 0.7784 (m110) REVERT: A 436 GLN cc_start: 0.7982 (mm110) cc_final: 0.7585 (mp-120) REVERT: A 541 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7346 (mptt) REVERT: A 586 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7654 (mt-10) outliers start: 12 outliers final: 7 residues processed: 53 average time/residue: 1.1387 time to fit residues: 62.9675 Evaluate side-chains 55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 444 LEU Chi-restraints excluded: chain A residue 541 LYS 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 48 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.127055 restraints weight = 4497.493| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 0.76 r_work: 0.3170 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4489 Z= 0.129 Angle : 0.467 5.928 6126 Z= 0.248 Chirality : 0.039 0.130 688 Planarity : 0.005 0.052 743 Dihedral : 3.865 21.265 605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.38), residues: 538 helix: 1.99 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.26 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.009 0.001 PHE A 335 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 301 *********************** 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 63 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.445 Fit side-chains REVERT: A 206 LYS cc_start: 0.7824 (ptpt) cc_final: 0.7337 (pttp) REVERT: A 329 PHE cc_start: 0.7978 (m-80) cc_final: 0.7533 (t80) REVERT: A 375 ASN cc_start: 0.8020 (m-40) cc_final: 0.7603 (m110) REVERT: A 377 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: A 436 GLN cc_start: 0.7866 (mm110) cc_final: 0.7465 (mp-120) REVERT: A 586 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7967 (mp0) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 1.1580 time to fit residues: 68.7910 Evaluate side-chains 56 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR 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 586 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.134519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.122277 restraints weight = 4518.258| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.77 r_work: 0.3074 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4489 Z= 0.166 Angle : 0.513 6.512 6126 Z= 0.273 Chirality : 0.040 0.125 688 Planarity : 0.005 0.055 743 Dihedral : 4.090 21.802 605 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.06 % Allowed : 12.04 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.38), residues: 538 helix: 1.98 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.015 0.001 PHE A 409 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 301 *********************** 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 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.445 Fit side-chains REVERT: A 206 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7323 (pttp) REVERT: A 329 PHE cc_start: 0.8065 (m-80) cc_final: 0.7548 (t80) REVERT: A 375 ASN cc_start: 0.8102 (m-40) cc_final: 0.7678 (m110) REVERT: A 377 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 436 GLN cc_start: 0.7941 (mm110) cc_final: 0.7535 (mp-120) REVERT: A 541 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7366 (mptt) REVERT: A 586 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7636 (mt-10) outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 1.1701 time to fit residues: 65.8836 Evaluate side-chains 55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR 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 22 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.133043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.120611 restraints weight = 4457.387| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 0.76 r_work: 0.3059 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4489 Z= 0.207 Angle : 0.562 6.630 6126 Z= 0.300 Chirality : 0.042 0.139 688 Planarity : 0.005 0.057 743 Dihedral : 4.372 22.048 605 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.41 % Allowed : 12.69 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.38), residues: 538 helix: 1.98 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.02 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 585 HIS 0.004 0.001 HIS A 280 PHE 0.018 0.002 PHE A 409 TYR 0.018 0.002 TYR A 84 ARG 0.003 0.001 ARG A 301 *********************** 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 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.588 Fit side-chains REVERT: A 206 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7428 (ptmt) REVERT: A 329 PHE cc_start: 0.8090 (m-80) cc_final: 0.7555 (t80) REVERT: A 375 ASN cc_start: 0.8194 (m-40) cc_final: 0.7838 (m110) REVERT: A 436 GLN cc_start: 0.7944 (mm110) cc_final: 0.7563 (mp-120) REVERT: A 541 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7440 (mptt) REVERT: A 586 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7792 (mt-10) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 2.1053 time to fit residues: 122.2620 Evaluate side-chains 55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 541 LYS 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 46 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.134161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.121470 restraints weight = 4515.658| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 0.81 r_work: 0.3083 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 4489 Z= 0.164 Angle : 0.515 6.516 6126 Z= 0.275 Chirality : 0.040 0.130 688 Planarity : 0.005 0.057 743 Dihedral : 4.174 21.774 605 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.19 % Allowed : 12.91 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.38), residues: 538 helix: 2.06 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -1.08 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE A 409 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 301 *********************** 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 55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 1.486 Fit side-chains REVERT: A 206 LYS cc_start: 0.7898 (ptpt) cc_final: 0.7327 (pttp) REVERT: A 329 PHE cc_start: 0.8017 (m-80) cc_final: 0.7525 (t80) REVERT: A 375 ASN cc_start: 0.8101 (m-40) cc_final: 0.7736 (m110) REVERT: A 436 GLN cc_start: 0.7905 (mm110) cc_final: 0.7516 (mp-120) REVERT: A 541 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7360 (mptt) REVERT: A 586 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7669 (mt-10) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 1.7094 time to fit residues: 93.8130 Evaluate side-chains 53 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 444 LEU 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 25 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 41 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.132985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.120697 restraints weight = 4441.522| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.77 r_work: 0.3095 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4489 Z= 0.186 Angle : 0.541 6.662 6126 Z= 0.289 Chirality : 0.041 0.130 688 Planarity : 0.005 0.058 743 Dihedral : 4.299 21.988 605 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.97 % Allowed : 13.79 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.38), residues: 538 helix: 2.02 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.10 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 PHE 0.016 0.002 PHE A 409 TYR 0.017 0.001 TYR A 84 ARG 0.003 0.000 ARG A 301 ********************** 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 53 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.474 Fit side-chains REVERT: A 206 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7356 (pttp) REVERT: A 329 PHE cc_start: 0.8014 (m-80) cc_final: 0.7557 (t80) REVERT: A 375 ASN cc_start: 0.8152 (m-40) cc_final: 0.7788 (m110) REVERT: A 436 GLN cc_start: 0.7867 (mm110) cc_final: 0.7495 (mp-120) REVERT: A 541 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7371 (mptt) REVERT: A 586 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7672 (mt-10) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 1.1256 time to fit residues: 58.7969 Evaluate side-chains 53 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 444 LEU 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 23 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.134576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122411 restraints weight = 4515.156| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 0.75 r_work: 0.3078 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4489 Z= 0.158 Angle : 0.509 6.176 6126 Z= 0.271 Chirality : 0.040 0.131 688 Planarity : 0.005 0.057 743 Dihedral : 4.114 21.671 605 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 13.35 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.38), residues: 538 helix: 2.18 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.05 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 585 HIS 0.003 0.001 HIS A 280 PHE 0.012 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.93 seconds wall clock time: 66 minutes 0.49 seconds (3960.49 seconds total)