Starting phenix.real_space_refine on Tue Jan 14 00:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vzo_43684/01_2025/8vzo_43684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vzo_43684/01_2025/8vzo_43684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vzo_43684/01_2025/8vzo_43684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vzo_43684/01_2025/8vzo_43684.map" model { file = "/net/cci-nas-00/data/ceres_data/8vzo_43684/01_2025/8vzo_43684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vzo_43684/01_2025/8vzo_43684.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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 26 5.16 5 C 3152 2.51 5 N 765 2.21 5 O 853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3235 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 15, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1013 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 541 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.99, per 1000 atoms: 0.83 Number of scatterers: 4796 At special positions: 0 Unit cell: (74.7, 64.74, 106.24, 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 26 16.00 O 853 8.00 N 765 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 584.3 milliseconds 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 5 sheets defined 62.0% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.952A pdb=" N VAL A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.522A pdb=" N ASN A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.815A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.982A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.541A pdb=" N ILE A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 216 removed outlier: 3.582A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 214 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.516A pdb=" N CYS A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.674A pdb=" N ALA A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 275 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.617A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 362 removed outlier: 4.553A pdb=" N ASN A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ARG A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 395 removed outlier: 3.716A pdb=" N LYS A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 423 through 453 removed outlier: 4.184A pdb=" N LEU A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 457 through 488 removed outlier: 3.639A pdb=" N ASN A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 removed outlier: 3.530A pdb=" N GLY A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.719A pdb=" N THR B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.968A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.544A pdb=" N LEU B 21 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.225A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 121 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.225A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.444A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 63 through 68 329 hydrogen bonds defined for protein. 948 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: 1.39 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 727 1.30 - 1.43: 1430 1.43 - 1.55: 2723 1.55 - 1.68: 2 1.68 - 1.81: 42 Bond restraints: 4924 Sorted by residual: bond pdb=" N PRO A 221 " pdb=" CD PRO A 221 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.11e+01 bond pdb=" CA SER A 194 " pdb=" CB SER A 194 " ideal model delta sigma weight residual 1.535 1.457 0.077 1.51e-02 4.39e+03 2.63e+01 bond pdb=" C HIS A 198 " pdb=" O HIS A 198 " ideal model delta sigma weight residual 1.236 1.170 0.065 1.28e-02 6.10e+03 2.61e+01 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.528 1.461 0.066 1.35e-02 5.49e+03 2.41e+01 bond pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 1.473 1.404 0.069 1.40e-02 5.10e+03 2.41e+01 ... (remaining 4919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5474 2.26 - 4.52: 1021 4.52 - 6.78: 162 6.78 - 9.04: 38 9.04 - 11.30: 5 Bond angle restraints: 6700 Sorted by residual: angle pdb=" N ASP B 93 " pdb=" CA ASP B 93 " pdb=" C ASP B 93 " ideal model delta sigma weight residual 112.88 102.80 10.08 1.29e+00 6.01e-01 6.11e+01 angle pdb=" N LYS A 329 " pdb=" CA LYS A 329 " pdb=" C LYS A 329 " ideal model delta sigma weight residual 113.17 103.46 9.71 1.26e+00 6.30e-01 5.93e+01 angle pdb=" CA PHE D 99 " pdb=" CB PHE D 99 " pdb=" CG PHE D 99 " ideal model delta sigma weight residual 113.80 121.01 -7.21 1.00e+00 1.00e+00 5.20e+01 angle pdb=" N GLY B 18 " pdb=" CA GLY B 18 " pdb=" C GLY B 18 " ideal model delta sigma weight residual 115.36 106.09 9.27 1.33e+00 5.65e-01 4.85e+01 angle pdb=" CA TYR A 397 " pdb=" C TYR A 397 " pdb=" N LYS A 398 " ideal model delta sigma weight residual 117.48 126.79 -9.31 1.41e+00 5.03e-01 4.36e+01 ... (remaining 6695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2544 17.52 - 35.03: 205 35.03 - 52.55: 56 52.55 - 70.07: 13 70.07 - 87.58: 7 Dihedral angle restraints: 2825 sinusoidal: 1053 harmonic: 1772 Sorted by residual: dihedral pdb=" CD ARG A 174 " pdb=" NE ARG A 174 " pdb=" CZ ARG A 174 " pdb=" NH1 ARG A 174 " ideal model delta sinusoidal sigma weight residual 0.00 -68.40 68.40 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " pdb=" CZ ARG B 90 " pdb=" NH1 ARG B 90 " ideal model delta sinusoidal sigma weight residual 0.00 57.15 -57.15 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CD ARG A 515 " pdb=" NE ARG A 515 " pdb=" CZ ARG A 515 " pdb=" NH1 ARG A 515 " ideal model delta sinusoidal sigma weight residual 0.00 44.54 -44.54 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 2822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 511 0.089 - 0.178: 187 0.178 - 0.267: 48 0.267 - 0.356: 13 0.356 - 0.445: 1 Chirality restraints: 760 Sorted by residual: chirality pdb=" CB VAL A 283 " pdb=" CA VAL A 283 " pdb=" CG1 VAL A 283 " pdb=" CG2 VAL A 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CB VAL B 8 " pdb=" CA VAL B 8 " pdb=" CG1 VAL B 8 " pdb=" CG2 VAL B 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASP D 83 " pdb=" N ASP D 83 " pdb=" C ASP D 83 " pdb=" CB ASP D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 757 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 1.013 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG A 174 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 90 " -0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG B 90 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG B 90 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 90 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 90 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 515 " 0.778 9.50e-02 1.11e+02 3.49e-01 7.39e+01 pdb=" NE ARG A 515 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 515 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 515 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 515 " 0.025 2.00e-02 2.50e+03 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1713 2.86 - 3.37: 4633 3.37 - 3.88: 8754 3.88 - 4.39: 10472 4.39 - 4.90: 16641 Nonbonded interactions: 42213 Sorted by model distance: nonbonded pdb=" O VAL A 414 " pdb=" OG1 THR A 418 " model vdw 2.347 3.040 nonbonded pdb=" OG SER B 20 " pdb=" O ASN B 87 " model vdw 2.381 3.040 nonbonded pdb=" N PHE B 30 " pdb=" O PHE B 30 " model vdw 2.407 2.496 nonbonded pdb=" N PHE B 107 " pdb=" O PHE B 107 " model vdw 2.414 2.496 nonbonded pdb=" O ALA A 306 " pdb=" OH TYR A 454 " model vdw 2.425 3.040 ... (remaining 42208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.910 Find NCS groups from input model: 0.050 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.013 0.078 4924 Z= 0.857 Angle : 1.822 11.298 6700 Z= 1.331 Chirality : 0.100 0.445 760 Planarity : 0.030 0.454 822 Dihedral : 14.971 87.582 1694 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.67 % Allowed : 9.65 % Favored : 86.68 % Cbeta Deviations : 0.18 % 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: -2.36 (0.30), residues: 607 helix: -1.53 (0.24), residues: 345 sheet: -0.13 (0.59), residues: 77 loop : -1.90 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 122 HIS 0.014 0.002 HIS A 198 PHE 0.042 0.003 PHE D 99 TYR 0.036 0.003 TYR B 57 ARG 0.004 0.001 ARG A 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.501 Fit side-chains REVERT: A 101 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 102 LYS cc_start: 0.7064 (tttt) cc_final: 0.6563 (tttm) REVERT: A 300 LYS cc_start: 0.7833 (tttp) cc_final: 0.7614 (tttp) REVERT: A 365 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 371 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7472 (mtt180) REVERT: A 393 LYS cc_start: 0.7030 (ttpt) cc_final: 0.6370 (tttt) outliers start: 19 outliers final: 4 residues processed: 99 average time/residue: 1.0864 time to fit residues: 112.5147 Evaluate side-chains 61 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 133 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 332 ASN A 368 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 520 ASN B 85 GLN D 38 GLN D 80 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127125 restraints weight = 4870.466| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.03 r_work: 0.3309 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4924 Z= 0.238 Angle : 0.606 7.741 6700 Z= 0.326 Chirality : 0.043 0.168 760 Planarity : 0.005 0.041 822 Dihedral : 5.480 44.872 673 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.32 % Allowed : 12.55 % Favored : 85.14 % 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: 0.18 (0.31), residues: 607 helix: 0.88 (0.26), residues: 344 sheet: 0.58 (0.59), residues: 72 loop : -1.40 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 228 HIS 0.002 0.001 HIS B 38 PHE 0.015 0.002 PHE A 495 TYR 0.027 0.002 TYR A 117 ARG 0.005 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.487 Fit side-chains REVERT: A 102 LYS cc_start: 0.7759 (tttt) cc_final: 0.7359 (tttm) REVERT: A 305 ARG cc_start: 0.8173 (ttt-90) cc_final: 0.7969 (ttt90) REVERT: A 365 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 371 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8152 (mtt180) REVERT: A 393 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7171 (tttm) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 1.1094 time to fit residues: 77.8123 Evaluate side-chains 62 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.166923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122191 restraints weight = 4803.448| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.71 r_work: 0.3299 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4924 Z= 0.212 Angle : 0.545 7.414 6700 Z= 0.293 Chirality : 0.042 0.170 760 Planarity : 0.005 0.040 822 Dihedral : 4.883 44.459 666 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.51 % Allowed : 12.93 % Favored : 84.56 % 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: 1.16 (0.32), residues: 607 helix: 1.67 (0.27), residues: 346 sheet: 0.78 (0.60), residues: 75 loop : -0.95 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.028 0.001 TYR A 117 ARG 0.003 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.586 Fit side-chains REVERT: A 102 LYS cc_start: 0.7729 (tttt) cc_final: 0.7255 (tttm) REVERT: A 155 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 365 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 371 ARG cc_start: 0.8377 (mtt180) cc_final: 0.8134 (mtt180) REVERT: A 393 LYS cc_start: 0.7790 (ttpt) cc_final: 0.7231 (tttm) REVERT: A 420 ASN cc_start: 0.8104 (p0) cc_final: 0.7771 (p0) outliers start: 13 outliers final: 3 residues processed: 62 average time/residue: 1.2024 time to fit residues: 77.8872 Evaluate side-chains 56 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.166807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121933 restraints weight = 4877.839| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.72 r_work: 0.3264 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4924 Z= 0.200 Angle : 0.524 7.161 6700 Z= 0.280 Chirality : 0.042 0.173 760 Planarity : 0.005 0.038 822 Dihedral : 4.768 45.323 666 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.47 % Allowed : 12.36 % Favored : 84.17 % 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: 1.61 (0.33), residues: 607 helix: 2.02 (0.26), residues: 345 sheet: 0.95 (0.60), residues: 75 loop : -0.69 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.028 0.001 TYR A 117 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.554 Fit side-chains REVERT: A 102 LYS cc_start: 0.7795 (tttt) cc_final: 0.7419 (ttpp) REVERT: A 155 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 371 ARG cc_start: 0.8453 (mtt180) cc_final: 0.8157 (mtm180) REVERT: A 393 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7285 (tttm) REVERT: A 419 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 420 ASN cc_start: 0.8095 (p0) cc_final: 0.7746 (p0) REVERT: B 119 MET cc_start: 0.8895 (mtt) cc_final: 0.8669 (mtt) outliers start: 18 outliers final: 7 residues processed: 58 average time/residue: 1.1941 time to fit residues: 72.5183 Evaluate side-chains 57 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 480 GLN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119786 restraints weight = 4889.457| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.73 r_work: 0.3271 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4924 Z= 0.245 Angle : 0.546 7.213 6700 Z= 0.292 Chirality : 0.043 0.180 760 Planarity : 0.005 0.040 822 Dihedral : 4.897 47.797 666 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.47 % Allowed : 12.16 % Favored : 84.36 % 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: 1.68 (0.33), residues: 607 helix: 1.92 (0.26), residues: 349 sheet: 1.13 (0.61), residues: 75 loop : -0.43 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.003 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.029 0.002 TYR A 117 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.492 Fit side-chains REVERT: A 102 LYS cc_start: 0.7799 (tttt) cc_final: 0.7355 (tttm) REVERT: A 371 ARG cc_start: 0.8407 (mtt180) cc_final: 0.8058 (mtm180) REVERT: A 393 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7319 (tttm) REVERT: A 419 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 420 ASN cc_start: 0.8085 (p0) cc_final: 0.7740 (p0) REVERT: B 119 MET cc_start: 0.8870 (mtt) cc_final: 0.8658 (mtt) outliers start: 18 outliers final: 7 residues processed: 58 average time/residue: 1.1881 time to fit residues: 72.1238 Evaluate side-chains 57 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.0030 chunk 20 optimal weight: 0.0770 overall best weight: 0.3148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 422 ASN A 480 GLN A 482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126901 restraints weight = 4899.206| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.05 r_work: 0.3265 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4924 Z= 0.154 Angle : 0.485 6.589 6700 Z= 0.258 Chirality : 0.040 0.165 760 Planarity : 0.004 0.038 822 Dihedral : 4.483 43.590 666 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.51 % Allowed : 14.29 % Favored : 83.20 % 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: 2.23 (0.33), residues: 607 helix: 2.41 (0.26), residues: 348 sheet: 1.44 (0.62), residues: 75 loop : -0.33 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.002 0.001 HIS A 361 PHE 0.017 0.001 PHE A 495 TYR 0.026 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.415 Fit side-chains REVERT: A 102 LYS cc_start: 0.7771 (tttt) cc_final: 0.7442 (tttm) REVERT: A 371 ARG cc_start: 0.8491 (mtt180) cc_final: 0.8228 (mtt180) REVERT: A 393 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7307 (tttm) outliers start: 13 outliers final: 2 residues processed: 55 average time/residue: 1.3646 time to fit residues: 78.0889 Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 361 HIS A 422 ASN A 470 GLN A 480 GLN D 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117639 restraints weight = 4818.904| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.72 r_work: 0.3231 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4924 Z= 0.344 Angle : 0.594 7.516 6700 Z= 0.315 Chirality : 0.046 0.189 760 Planarity : 0.005 0.040 822 Dihedral : 5.038 50.148 666 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.28 % Allowed : 12.74 % Favored : 83.98 % 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: 1.81 (0.33), residues: 607 helix: 1.88 (0.26), residues: 348 sheet: 1.46 (0.63), residues: 75 loop : -0.18 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.003 0.001 HIS A 361 PHE 0.020 0.002 PHE A 495 TYR 0.030 0.002 TYR A 117 ARG 0.002 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.546 Fit side-chains REVERT: A 102 LYS cc_start: 0.7823 (tttt) cc_final: 0.7388 (tttm) REVERT: A 155 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8307 (mp) REVERT: A 371 ARG cc_start: 0.8420 (mtt180) cc_final: 0.8128 (mtt180) REVERT: A 393 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7389 (tttm) REVERT: A 420 ASN cc_start: 0.8063 (p0) cc_final: 0.7715 (p0) REVERT: B 86 MET cc_start: 0.7162 (mtm) cc_final: 0.6801 (mtp) outliers start: 17 outliers final: 7 residues processed: 54 average time/residue: 1.2631 time to fit residues: 71.6829 Evaluate side-chains 53 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN D 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.165257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123170 restraints weight = 4810.482| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.24 r_work: 0.3271 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4924 Z= 0.224 Angle : 0.535 6.950 6700 Z= 0.284 Chirality : 0.042 0.179 760 Planarity : 0.005 0.040 822 Dihedral : 4.816 47.597 666 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.33), residues: 607 helix: 2.06 (0.26), residues: 348 sheet: 1.52 (0.63), residues: 75 loop : -0.14 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.002 PHE A 495 TYR 0.028 0.002 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.536 Fit side-chains REVERT: A 102 LYS cc_start: 0.7750 (tttt) cc_final: 0.7357 (tttm) REVERT: A 371 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8050 (mtm180) REVERT: A 393 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7298 (tttm) REVERT: A 420 ASN cc_start: 0.7953 (p0) cc_final: 0.7606 (p0) outliers start: 14 outliers final: 8 residues processed: 51 average time/residue: 1.3545 time to fit residues: 72.1458 Evaluate side-chains 53 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 422 ASN A 470 GLN A 480 GLN D 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122255 restraints weight = 4788.495| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.69 r_work: 0.3256 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4924 Z= 0.172 Angle : 0.505 6.653 6700 Z= 0.268 Chirality : 0.041 0.170 760 Planarity : 0.004 0.038 822 Dihedral : 4.571 45.443 666 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.12 % Allowed : 14.09 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.35 (0.34), residues: 607 helix: 2.38 (0.26), residues: 347 sheet: 1.62 (0.63), residues: 75 loop : -0.05 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 425 HIS 0.002 0.001 HIS A 361 PHE 0.017 0.001 PHE A 495 TYR 0.027 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.503 Fit side-chains REVERT: A 102 LYS cc_start: 0.7808 (tttt) cc_final: 0.7426 (tttm) REVERT: A 371 ARG cc_start: 0.8478 (mtt180) cc_final: 0.8166 (mtm180) REVERT: A 393 LYS cc_start: 0.7793 (ttpt) cc_final: 0.7324 (tttm) REVERT: A 420 ASN cc_start: 0.7903 (p0) cc_final: 0.7544 (p0) REVERT: B 86 MET cc_start: 0.7036 (mtm) cc_final: 0.6728 (mtp) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 1.4207 time to fit residues: 76.8919 Evaluate side-chains 54 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 0.3980 chunk 53 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 422 ASN A 470 GLN A 480 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119884 restraints weight = 4776.086| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.70 r_work: 0.3109 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4924 Z= 0.234 Angle : 0.541 6.732 6700 Z= 0.287 Chirality : 0.043 0.181 760 Planarity : 0.005 0.040 822 Dihedral : 4.755 48.011 666 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.54 % Allowed : 14.67 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.14 (0.33), residues: 607 helix: 2.14 (0.26), residues: 348 sheet: 1.64 (0.63), residues: 75 loop : -0.05 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 425 HIS 0.002 0.001 HIS A 361 PHE 0.019 0.002 PHE A 495 TYR 0.029 0.002 TYR A 117 ARG 0.002 0.000 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.497 Fit side-chains REVERT: A 102 LYS cc_start: 0.7850 (tttt) cc_final: 0.7342 (tttm) REVERT: A 371 ARG cc_start: 0.8363 (mtt180) cc_final: 0.7988 (mtm180) REVERT: A 393 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7276 (tttm) REVERT: A 420 ASN cc_start: 0.7916 (p0) cc_final: 0.7570 (p0) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 1.3372 time to fit residues: 69.8743 Evaluate side-chains 53 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 422 ASN A 480 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124713 restraints weight = 4860.056| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.12 r_work: 0.3285 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4924 Z= 0.174 Angle : 0.505 6.459 6700 Z= 0.268 Chirality : 0.041 0.170 760 Planarity : 0.004 0.038 822 Dihedral : 4.545 45.438 666 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.35 % Allowed : 15.06 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.34), residues: 607 helix: 2.41 (0.26), residues: 347 sheet: 1.64 (0.63), residues: 75 loop : -0.01 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 425 HIS 0.002 0.001 HIS A 361 PHE 0.018 0.001 PHE A 495 TYR 0.027 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.24 seconds wall clock time: 72 minutes 26.39 seconds (4346.39 seconds total)