Starting phenix.real_space_refine on Fri May 9 15:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgz_44527/05_2025/9bgz_44527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgz_44527/05_2025/9bgz_44527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgz_44527/05_2025/9bgz_44527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgz_44527/05_2025/9bgz_44527.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgz_44527/05_2025/9bgz_44527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgz_44527/05_2025/9bgz_44527.cif" } resolution = 3.0 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= 0.019 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 1849 2.51 5 N 431 2.21 5 O 483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2783 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2783 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 14, 'TRANS': 354} Chain breaks: 2 Time building chain proxies: 2.65, per 1000 atoms: 0.95 Number of scatterers: 2783 At special positions: 0 Unit cell: (68.475, 61.875, 70.95, 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 483 8.00 N 431 7.00 C 1849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 401.0 milliseconds 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.531A pdb=" N GLU A 26 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 23 through 27' Processing helix chain 'A' and resid 28 through 41 removed outlier: 3.853A pdb=" N GLY A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.790A pdb=" N GLY A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 93 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 154 Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.568A pdb=" N LYS A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 198 through 223 Proline residue: A 204 - end of helix removed outlier: 5.541A pdb=" N LYS A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 235 through 254 removed outlier: 3.686A pdb=" N PHE A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLU A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Proline residue: A 261 - end of helix removed outlier: 3.701A pdb=" N GLU A 268 " --> pdb=" O MET A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 289 through 307 Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.570A pdb=" N VAL A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 4.049A pdb=" N VAL A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 removed outlier: 4.270A pdb=" N LEU A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 389 removed outlier: 3.625A pdb=" N LEU A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.84 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: 837 1.34 - 1.46: 595 1.46 - 1.58: 1360 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 2829 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.51e-01 bond pdb=" CG1 ILE A 364 " pdb=" CD1 ILE A 364 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.52e-01 bond pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " ideal model delta sigma weight residual 1.528 1.539 -0.010 1.66e-02 3.63e+03 3.80e-01 bond pdb=" CG PRO A 351 " pdb=" CD PRO A 351 " ideal model delta sigma weight residual 1.503 1.484 0.019 3.40e-02 8.65e+02 3.18e-01 ... (remaining 2824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 3614 0.96 - 1.93: 174 1.93 - 2.89: 26 2.89 - 3.86: 13 3.86 - 4.82: 10 Bond angle restraints: 3837 Sorted by residual: angle pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " ideal model delta sigma weight residual 114.10 118.92 -4.82 2.00e+00 2.50e-01 5.81e+00 angle pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " pdb=" CD GLU A 117 " ideal model delta sigma weight residual 112.60 116.48 -3.88 1.70e+00 3.46e-01 5.22e+00 angle pdb=" N MET A 122 " pdb=" CA MET A 122 " pdb=" C MET A 122 " ideal model delta sigma weight residual 112.89 110.42 2.47 1.24e+00 6.50e-01 3.96e+00 angle pdb=" N ILE A 42 " pdb=" CA ILE A 42 " pdb=" CB ILE A 42 " ideal model delta sigma weight residual 112.07 109.81 2.26 1.52e+00 4.33e-01 2.20e+00 angle pdb=" CA PRO A 351 " pdb=" CB PRO A 351 " pdb=" CG PRO A 351 " ideal model delta sigma weight residual 104.50 107.32 -2.82 1.90e+00 2.77e-01 2.20e+00 ... (remaining 3832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 1443 15.02 - 30.03: 173 30.03 - 45.04: 53 45.04 - 60.06: 17 60.06 - 75.07: 2 Dihedral angle restraints: 1688 sinusoidal: 637 harmonic: 1051 Sorted by residual: dihedral pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N MET A 122 " pdb=" CA MET A 122 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU A 119 " pdb=" C LEU A 119 " pdb=" N LEU A 120 " pdb=" CA LEU A 120 " ideal model delta harmonic sigma weight residual 180.00 164.42 15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CB MET A 76 " pdb=" CG MET A 76 " pdb=" SD MET A 76 " pdb=" CE MET A 76 " ideal model delta sinusoidal sigma weight residual -60.00 -0.12 -59.88 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 334 0.031 - 0.061: 101 0.061 - 0.092: 51 0.092 - 0.123: 6 0.123 - 0.154: 1 Chirality restraints: 493 Sorted by residual: chirality pdb=" CA ILE A 123 " pdb=" N ILE A 123 " pdb=" C ILE A 123 " pdb=" CB ILE A 123 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA VAL A 272 " pdb=" N VAL A 272 " pdb=" C VAL A 272 " pdb=" CB VAL A 272 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA PRO A 204 " pdb=" N PRO A 204 " pdb=" C PRO A 204 " pdb=" CB PRO A 204 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.61e-01 ... (remaining 490 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 117 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" CD GLU A 117 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 117 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 117 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 369 " 0.113 9.50e-02 1.11e+02 5.07e-02 1.60e+00 pdb=" NE ARG A 369 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 369 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 369 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 369 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 27 " -0.006 2.00e-02 2.50e+03 7.18e-03 9.03e-01 pdb=" CG PHE A 27 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 27 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 27 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 27 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 27 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 27 " -0.002 2.00e-02 2.50e+03 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 669 2.79 - 3.32: 3054 3.32 - 3.84: 4697 3.84 - 4.37: 5342 4.37 - 4.90: 9417 Nonbonded interactions: 23179 Sorted by model distance: nonbonded pdb=" N GLU A 268 " pdb=" OE1 GLU A 268 " model vdw 2.258 3.120 nonbonded pdb=" N GLU A 26 " pdb=" OE1 GLU A 26 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASN A 235 " pdb=" N LEU A 237 " model vdw 2.338 3.120 nonbonded pdb=" O MET A 264 " pdb=" OE1 GLU A 268 " model vdw 2.377 3.040 nonbonded pdb=" O ASN A 373 " pdb=" OD2 ASP A 377 " model vdw 2.414 3.040 ... (remaining 23174 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: 1.940 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 0.033 2829 Z= 0.133 Angle : 0.542 4.819 3837 Z= 0.287 Chirality : 0.036 0.154 493 Planarity : 0.004 0.051 458 Dihedral : 15.102 75.070 1012 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.66 % Allowed : 22.85 % Favored : 76.49 % 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 (0.45), residues: 363 helix: 1.72 (0.29), residues: 311 sheet: None (None), residues: 0 loop : 0.85 (1.03), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 PHE 0.016 0.001 PHE A 27 TYR 0.008 0.002 TYR A 184 ARG 0.003 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.14664 ( 230) hydrogen bonds : angle 5.62670 ( 690) covalent geometry : bond 0.00285 ( 2829) covalent geometry : angle 0.54189 ( 3837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8503 (t) cc_final: 0.8245 (p) REVERT: A 20 ILE cc_start: 0.8387 (mp) cc_final: 0.8077 (mt) REVERT: A 60 ASP cc_start: 0.6697 (t0) cc_final: 0.5491 (t70) REVERT: A 63 LYS cc_start: 0.8526 (tttt) cc_final: 0.8310 (tttt) REVERT: A 97 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8380 (ttmm) REVERT: A 180 LYS cc_start: 0.8691 (mttt) cc_final: 0.8304 (tttp) REVERT: A 214 LEU cc_start: 0.8645 (tp) cc_final: 0.8306 (tm) REVERT: A 237 LEU cc_start: 0.8464 (tm) cc_final: 0.8249 (tt) REVERT: A 244 LYS cc_start: 0.8342 (pttm) cc_final: 0.8064 (ptpp) REVERT: A 269 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 288 ASN cc_start: 0.8101 (t0) cc_final: 0.7742 (t0) REVERT: A 318 THR cc_start: 0.8628 (m) cc_final: 0.8400 (t) REVERT: A 321 LEU cc_start: 0.8315 (tt) cc_final: 0.8103 (tm) REVERT: A 322 THR cc_start: 0.8439 (m) cc_final: 0.8193 (t) REVERT: A 338 LEU cc_start: 0.8103 (tp) cc_final: 0.7872 (mt) REVERT: A 340 MET cc_start: 0.7786 (mpt) cc_final: 0.7456 (mtm) REVERT: A 343 MET cc_start: 0.7930 (ttm) cc_final: 0.7179 (mpt) outliers start: 2 outliers final: 2 residues processed: 91 average time/residue: 1.0078 time to fit residues: 94.0764 Evaluate side-chains 83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 14 optimal weight: 0.0970 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.105742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093523 restraints weight = 4377.012| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.61 r_work: 0.3173 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2829 Z= 0.162 Angle : 0.612 7.347 3837 Z= 0.305 Chirality : 0.041 0.158 493 Planarity : 0.004 0.036 458 Dihedral : 4.765 38.845 387 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.96 % Allowed : 19.54 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.44), residues: 363 helix: 1.62 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 0.60 (1.26), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 PHE 0.015 0.002 PHE A 164 TYR 0.010 0.002 TYR A 184 ARG 0.002 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 230) hydrogen bonds : angle 4.41421 ( 690) covalent geometry : bond 0.00388 ( 2829) covalent geometry : angle 0.61235 ( 3837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8668 (t) cc_final: 0.8410 (p) REVERT: A 62 LYS cc_start: 0.8820 (pptt) cc_final: 0.8571 (pptt) REVERT: A 131 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8063 (mpp) REVERT: A 156 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8276 (mttp) REVERT: A 179 MET cc_start: 0.8738 (mmm) cc_final: 0.8526 (mmp) REVERT: A 180 LYS cc_start: 0.8837 (mttt) cc_final: 0.8622 (mttm) REVERT: A 207 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8013 (mmmt) REVERT: A 214 LEU cc_start: 0.8777 (tp) cc_final: 0.8527 (tt) REVERT: A 230 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 237 LEU cc_start: 0.8620 (tm) cc_final: 0.8391 (tt) REVERT: A 322 THR cc_start: 0.8574 (m) cc_final: 0.8113 (m) REVERT: A 340 MET cc_start: 0.7926 (mpt) cc_final: 0.7621 (mtm) REVERT: A 343 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7350 (mpt) outliers start: 18 outliers final: 5 residues processed: 88 average time/residue: 1.0186 time to fit residues: 92.1015 Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 343 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 29 optimal weight: 0.0870 overall best weight: 0.2756 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.107244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094925 restraints weight = 4277.666| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.61 r_work: 0.3204 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2829 Z= 0.138 Angle : 0.586 8.854 3837 Z= 0.291 Chirality : 0.039 0.152 493 Planarity : 0.004 0.037 458 Dihedral : 3.944 19.343 383 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.96 % Allowed : 22.85 % Favored : 71.19 % 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: 2.19 (0.44), residues: 363 helix: 1.62 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.30 (1.21), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 192 HIS 0.001 0.000 HIS A 219 PHE 0.014 0.001 PHE A 27 TYR 0.012 0.002 TYR A 75 ARG 0.001 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 230) hydrogen bonds : angle 4.20271 ( 690) covalent geometry : bond 0.00321 ( 2829) covalent geometry : angle 0.58631 ( 3837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8691 (t) cc_final: 0.8457 (p) REVERT: A 62 LYS cc_start: 0.8779 (pptt) cc_final: 0.8514 (pptt) REVERT: A 131 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8138 (mpp) REVERT: A 156 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8205 (mttp) REVERT: A 179 MET cc_start: 0.8665 (mmm) cc_final: 0.8462 (mmp) REVERT: A 180 LYS cc_start: 0.8825 (mttt) cc_final: 0.8618 (mttm) REVERT: A 237 LEU cc_start: 0.8632 (tm) cc_final: 0.8376 (tt) REVERT: A 322 THR cc_start: 0.8587 (m) cc_final: 0.8131 (m) REVERT: A 340 MET cc_start: 0.8052 (mpt) cc_final: 0.7573 (mtm) REVERT: A 343 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7347 (mpt) REVERT: A 377 ASP cc_start: 0.7449 (m-30) cc_final: 0.7241 (m-30) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 1.0506 time to fit residues: 89.5770 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.0270 chunk 4 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.106866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094309 restraints weight = 4344.381| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.62 r_work: 0.3175 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2829 Z= 0.155 Angle : 0.594 7.342 3837 Z= 0.297 Chirality : 0.039 0.146 493 Planarity : 0.004 0.040 458 Dihedral : 4.003 20.001 383 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.30 % Allowed : 23.84 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.38 (0.44), residues: 363 helix: 1.73 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.74 (1.16), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 219 PHE 0.016 0.002 PHE A 27 TYR 0.010 0.002 TYR A 184 ARG 0.010 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 230) hydrogen bonds : angle 4.19630 ( 690) covalent geometry : bond 0.00372 ( 2829) covalent geometry : angle 0.59385 ( 3837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8673 (t) cc_final: 0.8471 (p) REVERT: A 62 LYS cc_start: 0.8792 (pttt) cc_final: 0.8511 (pptt) REVERT: A 117 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 119 LEU cc_start: 0.8533 (mm) cc_final: 0.8289 (mp) REVERT: A 131 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8164 (mpp) REVERT: A 156 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: A 179 MET cc_start: 0.8673 (mmm) cc_final: 0.8381 (mmp) REVERT: A 180 LYS cc_start: 0.8807 (mttt) cc_final: 0.8605 (mttm) REVERT: A 237 LEU cc_start: 0.8662 (tm) cc_final: 0.8399 (tt) REVERT: A 322 THR cc_start: 0.8588 (m) cc_final: 0.8168 (m) REVERT: A 340 MET cc_start: 0.8061 (mpt) cc_final: 0.7615 (mtm) REVERT: A 343 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7342 (mpt) REVERT: A 377 ASP cc_start: 0.7537 (m-30) cc_final: 0.7327 (m-30) outliers start: 13 outliers final: 5 residues processed: 84 average time/residue: 1.0340 time to fit residues: 89.3040 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 343 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.105955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093249 restraints weight = 4358.555| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.73 r_work: 0.3164 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2829 Z= 0.187 Angle : 0.613 6.580 3837 Z= 0.310 Chirality : 0.041 0.151 493 Planarity : 0.005 0.040 458 Dihedral : 4.143 21.623 383 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.96 % Allowed : 23.18 % Favored : 70.86 % 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: 2.15 (0.44), residues: 363 helix: 1.60 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.42 (1.15), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 219 PHE 0.017 0.002 PHE A 164 TYR 0.012 0.002 TYR A 184 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 230) hydrogen bonds : angle 4.35062 ( 690) covalent geometry : bond 0.00460 ( 2829) covalent geometry : angle 0.61268 ( 3837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8698 (t) cc_final: 0.8489 (p) REVERT: A 62 LYS cc_start: 0.8789 (pttt) cc_final: 0.8456 (pptt) REVERT: A 119 LEU cc_start: 0.8505 (mm) cc_final: 0.8259 (mp) REVERT: A 131 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8154 (mpp) REVERT: A 156 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8407 (mttp) REVERT: A 180 LYS cc_start: 0.8824 (mttt) cc_final: 0.8607 (mttm) REVERT: A 218 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 237 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8461 (tt) REVERT: A 322 THR cc_start: 0.8617 (m) cc_final: 0.8355 (t) REVERT: A 340 MET cc_start: 0.8077 (mpt) cc_final: 0.7646 (mtm) REVERT: A 343 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7437 (mpt) REVERT: A 377 ASP cc_start: 0.7598 (m-30) cc_final: 0.7382 (m-30) outliers start: 18 outliers final: 8 residues processed: 83 average time/residue: 1.1100 time to fit residues: 94.5790 Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.106355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.093733 restraints weight = 4406.469| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.63 r_work: 0.3170 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2829 Z= 0.174 Angle : 0.616 7.453 3837 Z= 0.311 Chirality : 0.041 0.153 493 Planarity : 0.004 0.040 458 Dihedral : 4.124 20.341 383 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.30 % Allowed : 24.83 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.44), residues: 363 helix: 1.60 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.36 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 PHE 0.015 0.002 PHE A 27 TYR 0.011 0.002 TYR A 184 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 230) hydrogen bonds : angle 4.33042 ( 690) covalent geometry : bond 0.00427 ( 2829) covalent geometry : angle 0.61606 ( 3837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8671 (t) cc_final: 0.8454 (p) REVERT: A 119 LEU cc_start: 0.8500 (mm) cc_final: 0.8245 (mp) REVERT: A 131 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8106 (mpp) REVERT: A 156 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8384 (mttp) REVERT: A 180 LYS cc_start: 0.8785 (mttt) cc_final: 0.8556 (mttm) REVERT: A 218 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 237 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 288 ASN cc_start: 0.8362 (t0) cc_final: 0.8149 (t0) REVERT: A 319 ILE cc_start: 0.8402 (mm) cc_final: 0.8198 (tp) REVERT: A 322 THR cc_start: 0.8618 (m) cc_final: 0.8353 (t) REVERT: A 340 MET cc_start: 0.8057 (mpt) cc_final: 0.7594 (mtm) REVERT: A 343 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7407 (mpt) REVERT: A 377 ASP cc_start: 0.7573 (m-30) cc_final: 0.7327 (m-30) outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 1.0957 time to fit residues: 92.2528 Evaluate side-chains 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 350 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.106105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093495 restraints weight = 4442.497| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.64 r_work: 0.3158 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2829 Z= 0.186 Angle : 0.645 7.293 3837 Z= 0.324 Chirality : 0.042 0.154 493 Planarity : 0.005 0.041 458 Dihedral : 4.201 20.474 383 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.64 % Allowed : 26.49 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.44), residues: 363 helix: 1.60 (0.28), residues: 315 sheet: None (None), residues: 0 loop : 0.32 (1.04), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 PHE 0.016 0.002 PHE A 27 TYR 0.011 0.002 TYR A 184 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 230) hydrogen bonds : angle 4.38197 ( 690) covalent geometry : bond 0.00460 ( 2829) covalent geometry : angle 0.64517 ( 3837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8683 (t) cc_final: 0.8460 (p) REVERT: A 62 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8491 (pptt) REVERT: A 119 LEU cc_start: 0.8555 (mm) cc_final: 0.8301 (mp) REVERT: A 131 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8117 (mpp) REVERT: A 156 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8387 (mttp) REVERT: A 180 LYS cc_start: 0.8832 (mttt) cc_final: 0.8630 (mttp) REVERT: A 237 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 322 THR cc_start: 0.8650 (m) cc_final: 0.8397 (t) REVERT: A 340 MET cc_start: 0.8037 (mpt) cc_final: 0.7604 (mtm) REVERT: A 343 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7453 (mpt) REVERT: A 377 ASP cc_start: 0.7597 (m-30) cc_final: 0.7369 (m-30) outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 1.0576 time to fit residues: 88.0230 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 350 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.0980 chunk 12 optimal weight: 0.0370 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 30 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.107637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095396 restraints weight = 4343.936| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.61 r_work: 0.3195 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2829 Z= 0.144 Angle : 0.646 7.772 3837 Z= 0.322 Chirality : 0.041 0.149 493 Planarity : 0.005 0.046 458 Dihedral : 4.089 19.176 383 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.64 % Allowed : 26.82 % Favored : 68.54 % 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: 2.30 (0.44), residues: 363 helix: 1.72 (0.29), residues: 314 sheet: None (None), residues: 0 loop : 0.58 (1.03), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 192 HIS 0.001 0.000 HIS A 5 PHE 0.017 0.001 PHE A 27 TYR 0.008 0.002 TYR A 184 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 230) hydrogen bonds : angle 4.22385 ( 690) covalent geometry : bond 0.00342 ( 2829) covalent geometry : angle 0.64581 ( 3837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8661 (t) cc_final: 0.8460 (p) REVERT: A 62 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8356 (pptt) REVERT: A 131 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8109 (mpp) REVERT: A 156 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: A 209 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 237 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 322 THR cc_start: 0.8608 (m) cc_final: 0.8354 (t) REVERT: A 340 MET cc_start: 0.8032 (mpt) cc_final: 0.7590 (mtm) REVERT: A 343 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7412 (mpt) outliers start: 14 outliers final: 7 residues processed: 80 average time/residue: 1.0321 time to fit residues: 84.8474 Evaluate side-chains 88 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.106385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094103 restraints weight = 4334.235| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.63 r_work: 0.3179 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2829 Z= 0.212 Angle : 0.730 12.055 3837 Z= 0.361 Chirality : 0.045 0.247 493 Planarity : 0.005 0.045 458 Dihedral : 4.317 20.155 383 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.96 % Allowed : 25.50 % Favored : 68.54 % 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: 1.94 (0.44), residues: 363 helix: 1.43 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.65 (1.09), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 219 PHE 0.018 0.002 PHE A 27 TYR 0.012 0.002 TYR A 184 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 230) hydrogen bonds : angle 4.42190 ( 690) covalent geometry : bond 0.00530 ( 2829) covalent geometry : angle 0.72997 ( 3837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8677 (t) cc_final: 0.8447 (p) REVERT: A 62 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8413 (pptt) REVERT: A 119 LEU cc_start: 0.8478 (mm) cc_final: 0.8249 (mp) REVERT: A 131 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8092 (mpp) REVERT: A 156 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8469 (mttp) REVERT: A 209 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 237 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8423 (tt) REVERT: A 322 THR cc_start: 0.8578 (m) cc_final: 0.8150 (m) REVERT: A 340 MET cc_start: 0.8133 (mpt) cc_final: 0.7708 (mtm) REVERT: A 343 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7400 (mpt) REVERT: A 377 ASP cc_start: 0.7694 (m-30) cc_final: 0.7480 (m-30) outliers start: 18 outliers final: 6 residues processed: 82 average time/residue: 1.0823 time to fit residues: 91.0883 Evaluate side-chains 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 343 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.0370 chunk 34 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.106859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094703 restraints weight = 4412.605| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.61 r_work: 0.3201 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2829 Z= 0.168 Angle : 0.677 8.224 3837 Z= 0.339 Chirality : 0.043 0.159 493 Planarity : 0.005 0.048 458 Dihedral : 4.277 19.178 383 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.31 % Allowed : 28.81 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.05 (0.44), residues: 363 helix: 1.53 (0.29), residues: 312 sheet: None (None), residues: 0 loop : 0.67 (1.01), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 PHE 0.019 0.002 PHE A 27 TYR 0.010 0.002 TYR A 184 ARG 0.005 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 230) hydrogen bonds : angle 4.30921 ( 690) covalent geometry : bond 0.00411 ( 2829) covalent geometry : angle 0.67733 ( 3837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8656 (t) cc_final: 0.8439 (p) REVERT: A 62 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8398 (pptt) REVERT: A 119 LEU cc_start: 0.8524 (mm) cc_final: 0.8297 (mp) REVERT: A 131 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: A 156 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8392 (mttp) REVERT: A 179 MET cc_start: 0.8688 (mmm) cc_final: 0.8402 (mtm) REVERT: A 209 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 237 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 287 ILE cc_start: 0.8264 (mt) cc_final: 0.7990 (mt) REVERT: A 322 THR cc_start: 0.8577 (m) cc_final: 0.8190 (m) REVERT: A 340 MET cc_start: 0.8102 (mpt) cc_final: 0.7807 (mtm) REVERT: A 377 ASP cc_start: 0.7693 (m-30) cc_final: 0.7483 (m-30) outliers start: 10 outliers final: 5 residues processed: 81 average time/residue: 1.1013 time to fit residues: 91.4891 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 268 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.0570 chunk 16 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.107337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095266 restraints weight = 4316.001| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.58 r_work: 0.3193 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2829 Z= 0.159 Angle : 0.669 7.769 3837 Z= 0.336 Chirality : 0.042 0.159 493 Planarity : 0.005 0.043 458 Dihedral : 4.232 19.183 383 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.30 % Allowed : 27.48 % Favored : 68.21 % 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: 2.07 (0.44), residues: 363 helix: 1.53 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 0.73 (1.06), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 219 PHE 0.018 0.002 PHE A 27 TYR 0.009 0.002 TYR A 184 ARG 0.005 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 230) hydrogen bonds : angle 4.29052 ( 690) covalent geometry : bond 0.00388 ( 2829) covalent geometry : angle 0.66943 ( 3837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.08 seconds wall clock time: 45 minutes 25.20 seconds (2725.20 seconds total)