Starting phenix.real_space_refine on Sat Apr 26 17:33:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgz_44527/04_2025/9bgz_44527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgz_44527/04_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_44527/04_2025/9bgz_44527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgz_44527/04_2025/9bgz_44527.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgz_44527/04_2025/9bgz_44527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgz_44527/04_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-5669/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: 2.72, per 1000 atoms: 0.98 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: 0.76 Conformation dependent library (CDL) restraints added in 350.4 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: 0.29 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: 0.84 Time building geometry restraints manager: 0.91 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.880 Find NCS groups from input model: 0.030 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- 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 : 0.292 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: 1.0106 time to fit residues: 94.4518 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 : 0.301 ------------------------------------------------------------------------------- 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 = 0.093522 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: 0.3037 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- 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 : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8669 (t) cc_final: 0.8410 (p) REVERT: A 62 LYS cc_start: 0.8823 (pptt) cc_final: 0.8574 (pptt) REVERT: A 131 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8061 (mpp) REVERT: A 156 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8277 (mttp) REVERT: A 179 MET cc_start: 0.8737 (mmm) cc_final: 0.8525 (mmp) REVERT: A 180 LYS cc_start: 0.8841 (mttt) cc_final: 0.8627 (mttm) REVERT: A 207 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8015 (mmmt) REVERT: A 214 LEU cc_start: 0.8778 (tp) cc_final: 0.8528 (tt) REVERT: A 230 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: A 237 LEU cc_start: 0.8621 (tm) cc_final: 0.8392 (tt) REVERT: A 322 THR cc_start: 0.8575 (m) cc_final: 0.8114 (m) REVERT: A 340 MET cc_start: 0.7925 (mpt) cc_final: 0.7620 (mtm) REVERT: A 343 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7352 (mpt) outliers start: 18 outliers final: 5 residues processed: 88 average time/residue: 0.9782 time to fit residues: 88.5347 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 : 0.328 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 29 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.106324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093842 restraints weight = 4237.351| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.68 r_work: 0.3188 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2180 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= 0.164 Angle : 0.604 8.760 3837 Z= 0.302 Chirality : 0.040 0.146 493 Planarity : 0.004 0.037 458 Dihedral : 4.060 20.608 383 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 2.30 (0.44), residues: 363 helix: 1.65 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.97 (1.22), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.001 0.001 HIS A 5 PHE 0.015 0.002 PHE A 27 TYR 0.012 0.002 TYR A 75 ARG 0.002 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 230) hydrogen bonds : angle 4.32085 ( 690) covalent geometry : bond 0.00397 ( 2829) covalent geometry : angle 0.60381 ( 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 94 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8719 (t) cc_final: 0.8475 (p) REVERT: A 62 LYS cc_start: 0.8782 (pptt) cc_final: 0.8501 (pptt) REVERT: A 119 LEU cc_start: 0.8426 (mm) cc_final: 0.8173 (mp) REVERT: A 131 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8126 (mpp) REVERT: A 156 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8345 (mttp) REVERT: A 180 LYS cc_start: 0.8833 (mttt) cc_final: 0.8617 (mttm) REVERT: A 237 LEU cc_start: 0.8639 (tm) cc_final: 0.8395 (tt) REVERT: A 322 THR cc_start: 0.8600 (m) cc_final: 0.8158 (m) REVERT: A 340 MET cc_start: 0.8100 (mpt) cc_final: 0.7703 (mtm) REVERT: A 343 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7375 (mpt) REVERT: A 377 ASP cc_start: 0.7525 (m-30) cc_final: 0.7308 (m-30) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 1.0483 time to fit residues: 89.3539 Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 222 ILE Chi-restraints excluded: chain A residue 268 GLU 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: 0.3980 chunk 4 optimal weight: 0.0970 chunk 26 optimal weight: 0.0020 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 6 optimal weight: 0.6980 overall best weight: 0.1386 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.109461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.096928 restraints weight = 4353.606| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.64 r_work: 0.3239 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2829 Z= 0.117 Angle : 0.570 7.621 3837 Z= 0.281 Chirality : 0.038 0.142 493 Planarity : 0.004 0.040 458 Dihedral : 3.855 19.566 383 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.97 % Allowed : 23.84 % Favored : 72.19 % 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: 2.41 (0.44), residues: 363 helix: 1.78 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 0.28 (1.14), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 192 HIS 0.001 0.000 HIS A 5 PHE 0.016 0.001 PHE A 27 TYR 0.015 0.002 TYR A 75 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 230) hydrogen bonds : angle 4.03135 ( 690) covalent geometry : bond 0.00254 ( 2829) covalent geometry : angle 0.57017 ( 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 89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8705 (pttt) cc_final: 0.8416 (pptt) REVERT: A 131 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8114 (mpp) REVERT: A 237 LEU cc_start: 0.8638 (tm) cc_final: 0.8364 (tt) REVERT: A 322 THR cc_start: 0.8571 (m) cc_final: 0.8133 (m) REVERT: A 340 MET cc_start: 0.7980 (mpt) cc_final: 0.7613 (mtm) REVERT: A 343 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7310 (mpt) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 1.0659 time to fit residues: 90.9171 Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 325 LEU 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: 0.5980 chunk 22 optimal weight: 0.0870 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.107359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095131 restraints weight = 4361.107| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.62 r_work: 0.3193 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2535 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= 0.158 Angle : 0.603 6.820 3837 Z= 0.300 Chirality : 0.040 0.149 493 Planarity : 0.005 0.040 458 Dihedral : 3.979 19.405 383 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.96 % Allowed : 23.84 % Favored : 70.20 % 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: 2.38 (0.44), residues: 363 helix: 1.75 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.58 (1.10), 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 5 PHE 0.016 0.002 PHE A 27 TYR 0.016 0.002 TYR A 75 ARG 0.010 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 230) hydrogen bonds : angle 4.19107 ( 690) covalent geometry : bond 0.00386 ( 2829) covalent geometry : angle 0.60316 ( 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 : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8767 (pttt) cc_final: 0.8454 (pptt) REVERT: A 119 LEU cc_start: 0.8464 (mm) cc_final: 0.8206 (mp) REVERT: A 131 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8106 (mpp) REVERT: A 156 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8258 (mttp) REVERT: A 179 MET cc_start: 0.8741 (mmm) cc_final: 0.8515 (mmp) REVERT: A 218 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 237 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8389 (tt) REVERT: A 322 THR cc_start: 0.8577 (m) cc_final: 0.8330 (t) REVERT: A 340 MET cc_start: 0.8085 (mpt) cc_final: 0.7600 (mtm) REVERT: A 343 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7323 (mpt) REVERT: A 377 ASP cc_start: 0.7618 (m-30) cc_final: 0.7405 (m-30) outliers start: 18 outliers final: 7 residues processed: 83 average time/residue: 1.0259 time to fit residues: 87.5162 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 : 0.294 ------------------------------------------------------------------------------- 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 343 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.106141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093429 restraints weight = 4408.693| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.74 r_work: 0.3164 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2675 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 : 0.624 6.990 3837 Z= 0.311 Chirality : 0.041 0.151 493 Planarity : 0.005 0.039 458 Dihedral : 4.140 20.931 383 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.63 % Allowed : 24.50 % 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: 2.11 (0.44), residues: 363 helix: 1.58 (0.28), residues: 322 sheet: None (None), residues: 0 loop : 0.35 (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 219 PHE 0.017 0.002 PHE A 164 TYR 0.020 0.002 TYR A 75 ARG 0.009 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 230) hydrogen bonds : angle 4.31982 ( 690) covalent geometry : bond 0.00459 ( 2829) covalent geometry : angle 0.62432 ( 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 93 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8447 (pptt) REVERT: A 119 LEU cc_start: 0.8513 (mm) cc_final: 0.8259 (mp) REVERT: A 131 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8144 (mpp) REVERT: A 156 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: A 179 MET cc_start: 0.8728 (mmm) cc_final: 0.8501 (mmp) REVERT: A 218 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 237 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8467 (tt) REVERT: A 318 THR cc_start: 0.8419 (m) cc_final: 0.7956 (p) REVERT: A 322 THR cc_start: 0.8594 (m) cc_final: 0.8175 (m) REVERT: A 340 MET cc_start: 0.8095 (mpt) cc_final: 0.7702 (mtm) REVERT: A 343 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7396 (mpt) REVERT: A 377 ASP cc_start: 0.7738 (m-30) cc_final: 0.7516 (m-30) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 1.1134 time to fit residues: 95.9667 Evaluate side-chains 87 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 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: 0.0040 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.106956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.094490 restraints weight = 4458.043| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.64 r_work: 0.3176 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2738 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= 0.157 Angle : 0.606 7.360 3837 Z= 0.303 Chirality : 0.040 0.148 493 Planarity : 0.004 0.040 458 Dihedral : 4.092 19.645 383 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.64 % Allowed : 25.17 % Favored : 70.20 % 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: 2.19 (0.44), residues: 363 helix: 1.64 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.34 (1.08), residues: 42 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 0.002 PHE A 27 TYR 0.016 0.002 TYR A 75 ARG 0.008 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 230) hydrogen bonds : angle 4.22236 ( 690) covalent geometry : bond 0.00381 ( 2829) covalent geometry : angle 0.60579 ( 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 : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8556 (mm) cc_final: 0.8302 (mp) REVERT: A 131 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8140 (mpp) REVERT: A 156 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8329 (mttp) REVERT: A 179 MET cc_start: 0.8709 (mmm) cc_final: 0.8500 (mmp) REVERT: A 209 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 237 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8472 (tt) REVERT: A 322 THR cc_start: 0.8546 (m) cc_final: 0.8149 (m) REVERT: A 340 MET cc_start: 0.8048 (mpt) cc_final: 0.7772 (mtm) REVERT: A 343 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7383 (mpt) REVERT: A 377 ASP cc_start: 0.7684 (m-30) cc_final: 0.7463 (m-30) outliers start: 14 outliers final: 8 residues processed: 80 average time/residue: 1.1270 time to fit residues: 92.5695 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 202 LEU Chi-restraints excluded: chain A residue 209 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 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: 0.3980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.106583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094114 restraints weight = 4350.941| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.62 r_work: 0.3177 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2807 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 : 0.637 7.325 3837 Z= 0.318 Chirality : 0.041 0.156 493 Planarity : 0.005 0.040 458 Dihedral : 4.149 19.934 383 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.30 % Allowed : 26.49 % 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: 2.05 (0.44), residues: 363 helix: 1.54 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.35 (1.08), 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 0.018 0.002 PHE A 27 TYR 0.020 0.002 TYR A 75 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 230) hydrogen bonds : angle 4.25936 ( 690) covalent geometry : bond 0.00425 ( 2829) covalent geometry : angle 0.63667 ( 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: 16 poor density : 73 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8512 (mm) cc_final: 0.8251 (mp) REVERT: A 131 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8084 (mpp) REVERT: A 156 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8359 (mttp) REVERT: A 179 MET cc_start: 0.8713 (mmm) cc_final: 0.8509 (mmp) REVERT: A 209 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 237 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 322 THR cc_start: 0.8494 (m) cc_final: 0.8100 (m) REVERT: A 340 MET cc_start: 0.8040 (mpt) cc_final: 0.7713 (mtm) REVERT: A 343 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7388 (mpt) REVERT: A 377 ASP cc_start: 0.7690 (m-30) cc_final: 0.7461 (m-30) outliers start: 16 outliers final: 10 residues processed: 78 average time/residue: 1.1207 time to fit residues: 89.7141 Evaluate side-chains 88 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 202 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.106258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093990 restraints weight = 4333.079| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.59 r_work: 0.3176 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2874 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= 0.184 Angle : 0.652 7.323 3837 Z= 0.328 Chirality : 0.042 0.156 493 Planarity : 0.005 0.040 458 Dihedral : 4.191 20.086 383 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.30 % Allowed : 26.49 % 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: 1.99 (0.44), residues: 363 helix: 1.48 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.51 (1.10), 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 5 PHE 0.019 0.002 PHE A 27 TYR 0.023 0.002 TYR A 75 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 230) hydrogen bonds : angle 4.30704 ( 690) covalent geometry : bond 0.00456 ( 2829) covalent geometry : angle 0.65193 ( 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 92 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8512 (mm) cc_final: 0.8249 (mp) REVERT: A 131 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8093 (mpp) REVERT: A 156 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8387 (mttp) REVERT: A 179 MET cc_start: 0.8697 (mmm) cc_final: 0.8492 (mmp) REVERT: A 209 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 237 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8437 (tt) REVERT: A 322 THR cc_start: 0.8498 (m) cc_final: 0.8120 (m) REVERT: A 340 MET cc_start: 0.8047 (mpt) cc_final: 0.7722 (mtm) REVERT: A 377 ASP cc_start: 0.7702 (m-30) cc_final: 0.7472 (m-30) outliers start: 16 outliers final: 9 residues processed: 81 average time/residue: 1.0906 time to fit residues: 90.6478 Evaluate side-chains 87 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 202 LEU 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 265 ARG 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 31 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.106318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093922 restraints weight = 4442.170| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.61 r_work: 0.3172 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2879 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 : 0.670 7.561 3837 Z= 0.336 Chirality : 0.042 0.156 493 Planarity : 0.005 0.063 458 Dihedral : 4.220 20.374 383 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.64 % Allowed : 28.15 % Favored : 67.22 % 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: 1.77 (0.44), residues: 363 helix: 1.35 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.30 (1.08), 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 0.020 0.002 PHE A 27 TYR 0.026 0.002 TYR A 75 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 230) hydrogen bonds : angle 4.36171 ( 690) covalent geometry : bond 0.00458 ( 2829) covalent geometry : angle 0.67040 ( 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 88 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8461 (pptt) REVERT: A 119 LEU cc_start: 0.8526 (mm) cc_final: 0.8256 (mp) REVERT: A 131 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8101 (mpp) REVERT: A 156 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8394 (mttp) REVERT: A 179 MET cc_start: 0.8694 (mmm) cc_final: 0.8490 (mmp) REVERT: A 237 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 322 THR cc_start: 0.8504 (m) cc_final: 0.8101 (m) REVERT: A 340 MET cc_start: 0.8036 (mpt) cc_final: 0.7704 (mtm) REVERT: A 377 ASP cc_start: 0.7729 (m-30) cc_final: 0.7498 (m-30) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 1.0800 time to fit residues: 87.5843 Evaluate side-chains 84 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 202 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.1980 chunk 31 optimal weight: 0.4980 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.107239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094937 restraints weight = 4367.834| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.61 r_work: 0.3196 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2829 Z= 0.142 Angle : 0.638 7.726 3837 Z= 0.319 Chirality : 0.041 0.158 493 Planarity : 0.005 0.042 458 Dihedral : 4.084 19.449 383 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 4.30 % Allowed : 28.48 % Favored : 67.22 % 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: 2.11 (0.45), residues: 363 helix: 1.55 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.74 (1.10), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 192 HIS 0.001 0.000 HIS A 219 PHE 0.019 0.002 PHE A 27 TYR 0.027 0.002 TYR A 75 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 230) hydrogen bonds : angle 4.22537 ( 690) covalent geometry : bond 0.00334 ( 2829) covalent geometry : angle 0.63849 ( 3837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.47 seconds wall clock time: 48 minutes 25.20 seconds (2905.20 seconds total)