Starting phenix.real_space_refine on Wed Sep 17 03:17:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgz_44527/09_2025/9bgz_44527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgz_44527/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bgz_44527/09_2025/9bgz_44527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgz_44527/09_2025/9bgz_44527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bgz_44527/09_2025/9bgz_44527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgz_44527/09_2025/9bgz_44527.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.79, per 1000 atoms: 0.28 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: 0.23 Conformation dependent library (CDL) restraints added in 103.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.08 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: 0.29 Time building geometry restraints manager: 0.32 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: 4.480 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.250 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.000 ARG A 369 TYR 0.008 0.002 TYR A 184 PHE 0.016 0.001 PHE A 27 TRP 0.001 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 2829) covalent geometry : angle 0.54189 ( 3837) hydrogen bonds : bond 0.14664 ( 230) hydrogen bonds : angle 5.62670 ( 690) *********************** 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 : 0.075 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: 0.4719 time to fit residues: 43.9878 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 : 0.102 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.0040 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.105305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092966 restraints weight = 4384.166| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.71 r_work: 0.3163 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1728 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= 0.171 Angle : 0.616 7.098 3837 Z= 0.308 Chirality : 0.041 0.144 493 Planarity : 0.004 0.036 458 Dihedral : 4.763 37.964 387 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.63 % Allowed : 19.54 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.45), residues: 363 helix: 1.59 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.60 (1.30), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 37 TYR 0.011 0.002 TYR A 184 PHE 0.015 0.002 PHE A 164 TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 2829) covalent geometry : angle 0.61622 ( 3837) hydrogen bonds : bond 0.04569 ( 230) hydrogen bonds : angle 4.46116 ( 690) *********************** 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 99 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8693 (t) cc_final: 0.8437 (p) REVERT: A 62 LYS cc_start: 0.8859 (pptt) cc_final: 0.8614 (pptt) REVERT: A 131 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8124 (mpp) REVERT: A 156 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: A 179 MET cc_start: 0.8728 (mmm) cc_final: 0.8518 (mmp) REVERT: A 180 LYS cc_start: 0.8869 (mttt) cc_final: 0.8661 (mttp) REVERT: A 207 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8019 (mmmt) REVERT: A 230 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: A 237 LEU cc_start: 0.8623 (tm) cc_final: 0.8400 (tt) REVERT: A 322 THR cc_start: 0.8570 (m) cc_final: 0.8112 (m) REVERT: A 340 MET cc_start: 0.7976 (mpt) cc_final: 0.7479 (mtm) REVERT: A 343 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7377 (mpt) outliers start: 17 outliers final: 6 residues processed: 87 average time/residue: 0.4593 time to fit residues: 41.0492 Evaluate side-chains 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 325 LEU 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 12 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 19 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.1896 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.107871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095627 restraints weight = 4388.791| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.62 r_work: 0.3209 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2829 Z= 0.126 Angle : 0.579 8.777 3837 Z= 0.285 Chirality : 0.038 0.144 493 Planarity : 0.004 0.037 458 Dihedral : 3.936 19.293 383 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.97 % Allowed : 24.50 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.44), residues: 363 helix: 1.70 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 0.37 (1.17), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.010 0.002 TYR A 4 PHE 0.015 0.001 PHE A 27 TRP 0.001 0.000 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2829) covalent geometry : angle 0.57910 ( 3837) hydrogen bonds : bond 0.03994 ( 230) hydrogen bonds : angle 4.16138 ( 690) *********************** 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 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8650 (t) cc_final: 0.8400 (p) REVERT: A 62 LYS cc_start: 0.8758 (pptt) cc_final: 0.8459 (pptt) REVERT: A 180 LYS cc_start: 0.8830 (mttt) cc_final: 0.8611 (mttp) REVERT: A 207 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7985 (mmmt) REVERT: A 237 LEU cc_start: 0.8609 (tm) cc_final: 0.8360 (tt) REVERT: A 281 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7601 (mp) REVERT: A 322 THR cc_start: 0.8527 (m) cc_final: 0.8070 (m) REVERT: A 340 MET cc_start: 0.8059 (mpt) cc_final: 0.7567 (mtm) REVERT: A 343 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7317 (mpt) REVERT: A 377 ASP cc_start: 0.7417 (m-30) cc_final: 0.7174 (m-30) outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.4767 time to fit residues: 39.6121 Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 281 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 20 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.105400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093058 restraints weight = 4363.945| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.70 r_work: 0.3165 rms_B_bonded: 2.32 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: 0.8176 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2829 Z= 0.192 Angle : 0.616 7.028 3837 Z= 0.310 Chirality : 0.041 0.145 493 Planarity : 0.004 0.041 458 Dihedral : 4.151 21.389 383 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.63 % Allowed : 23.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.44), residues: 363 helix: 1.64 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.85 (1.20), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.014 0.002 TYR A 75 PHE 0.017 0.002 PHE A 164 TRP 0.002 0.001 TRP A 192 HIS 0.000 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 2829) covalent geometry : angle 0.61606 ( 3837) hydrogen bonds : bond 0.04613 ( 230) hydrogen bonds : angle 4.37834 ( 690) *********************** 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: 17 poor density : 74 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 VAL cc_start: 0.8697 (t) cc_final: 0.8491 (p) REVERT: A 62 LYS cc_start: 0.8810 (pttt) cc_final: 0.8514 (pptt) REVERT: A 117 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: A 119 LEU cc_start: 0.8515 (mm) cc_final: 0.8276 (mp) REVERT: A 131 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8117 (mpp) REVERT: A 156 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8448 (mttp) REVERT: A 180 LYS cc_start: 0.8857 (mttt) cc_final: 0.8655 (mttm) REVERT: A 237 LEU cc_start: 0.8666 (tm) cc_final: 0.8423 (tt) REVERT: A 268 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: A 322 THR cc_start: 0.8618 (m) cc_final: 0.8198 (m) REVERT: A 340 MET cc_start: 0.8126 (mpt) cc_final: 0.7687 (mtm) REVERT: A 343 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7406 (mpt) REVERT: A 377 ASP cc_start: 0.7623 (m-30) cc_final: 0.7405 (m-30) outliers start: 17 outliers final: 6 residues processed: 81 average time/residue: 0.5067 time to fit residues: 42.0303 Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 97 LYS 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 276 ILE 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 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 31 optimal weight: 0.0070 chunk 22 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 overall best weight: 0.2556 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.107809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095427 restraints weight = 4313.301| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.61 r_work: 0.3196 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2540 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= 0.135 Angle : 0.581 6.828 3837 Z= 0.289 Chirality : 0.039 0.148 493 Planarity : 0.004 0.042 458 Dihedral : 4.014 19.500 383 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.30 % Allowed : 24.17 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.44), residues: 363 helix: 1.80 (0.28), residues: 320 sheet: None (None), residues: 0 loop : 0.76 (1.12), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.016 0.002 TYR A 75 PHE 0.015 0.001 PHE A 27 TRP 0.001 0.000 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2829) covalent geometry : angle 0.58111 ( 3837) hydrogen bonds : bond 0.04079 ( 230) hydrogen bonds : angle 4.20687 ( 690) *********************** 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 89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8766 (pttt) cc_final: 0.8471 (pptt) REVERT: A 119 LEU cc_start: 0.8526 (mm) cc_final: 0.8265 (mp) REVERT: A 131 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8118 (mpp) REVERT: A 156 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8208 (mttp) REVERT: A 237 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8410 (tt) REVERT: A 268 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 281 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 322 THR cc_start: 0.8598 (m) cc_final: 0.8178 (m) REVERT: A 340 MET cc_start: 0.8069 (mpt) cc_final: 0.7684 (mtm) REVERT: A 343 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7371 (mpt) REVERT: A 377 ASP cc_start: 0.7511 (m-30) cc_final: 0.7264 (m-30) outliers start: 16 outliers final: 6 residues processed: 81 average time/residue: 0.4964 time to fit residues: 41.2268 Evaluate side-chains 83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 PHE 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 268 GLU Chi-restraints excluded: chain A residue 281 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: 0.1980 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.1980 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.108796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.096359 restraints weight = 4319.779| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.61 r_work: 0.3214 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2829 Z= 0.122 Angle : 0.565 6.626 3837 Z= 0.281 Chirality : 0.039 0.150 493 Planarity : 0.004 0.040 458 Dihedral : 3.945 19.221 383 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.97 % Allowed : 26.49 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.44), residues: 363 helix: 1.71 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 0.35 (1.10), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.017 0.002 TYR A 75 PHE 0.014 0.001 PHE A 27 TRP 0.001 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2829) covalent geometry : angle 0.56471 ( 3837) hydrogen bonds : bond 0.03818 ( 230) hydrogen bonds : angle 4.08947 ( 690) *********************** 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 87 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8441 (pptt) REVERT: A 131 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8133 (mpp) REVERT: A 156 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8232 (mttp) REVERT: A 237 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8401 (tt) REVERT: A 268 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 281 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7660 (mp) REVERT: A 318 THR cc_start: 0.8490 (m) cc_final: 0.7995 (p) REVERT: A 322 THR cc_start: 0.8601 (m) cc_final: 0.8193 (m) REVERT: A 340 MET cc_start: 0.8010 (mpt) cc_final: 0.7599 (mtm) REVERT: A 343 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7367 (mpt) REVERT: A 377 ASP cc_start: 0.7484 (m-30) cc_final: 0.7284 (m-30) outliers start: 12 outliers final: 5 residues processed: 81 average time/residue: 0.5413 time to fit residues: 44.9352 Evaluate side-chains 83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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 202 LEU 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 281 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 14 optimal weight: 0.0670 chunk 15 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 overall best weight: 0.1152 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.110433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098093 restraints weight = 4348.419| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.61 r_work: 0.3241 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2817 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= 0.115 Angle : 0.575 6.641 3837 Z= 0.281 Chirality : 0.039 0.149 493 Planarity : 0.004 0.040 458 Dihedral : 3.830 19.393 383 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 5.30 % Allowed : 25.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.44), residues: 363 helix: 1.81 (0.29), residues: 326 sheet: None (None), residues: 0 loop : 0.48 (1.12), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.016 0.002 TYR A 75 PHE 0.015 0.001 PHE A 27 TRP 0.001 0.000 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 2829) covalent geometry : angle 0.57459 ( 3837) hydrogen bonds : bond 0.03615 ( 230) hydrogen bonds : angle 3.97681 ( 690) *********************** 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 91 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8390 (pptt) REVERT: A 131 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8100 (mpp) REVERT: A 156 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8181 (mttp) REVERT: A 209 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 237 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8375 (tt) REVERT: A 268 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: A 281 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7653 (mp) REVERT: A 318 THR cc_start: 0.8281 (m) cc_final: 0.7961 (p) REVERT: A 322 THR cc_start: 0.8578 (m) cc_final: 0.8340 (t) REVERT: A 340 MET cc_start: 0.7943 (mpt) cc_final: 0.7553 (mtm) REVERT: A 343 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7353 (mpt) REVERT: A 377 ASP cc_start: 0.7429 (m-30) cc_final: 0.7218 (m-30) outliers start: 16 outliers final: 4 residues processed: 83 average time/residue: 0.5152 time to fit residues: 43.8114 Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 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 268 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 343 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 10 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3316 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.107903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095574 restraints weight = 4408.737| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.63 r_work: 0.3197 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2829 Z= 0.149 Angle : 0.600 7.316 3837 Z= 0.294 Chirality : 0.040 0.156 493 Planarity : 0.004 0.038 458 Dihedral : 3.953 19.259 383 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.97 % Allowed : 26.82 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.44), residues: 363 helix: 1.85 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 0.79 (1.09), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.017 0.002 TYR A 75 PHE 0.016 0.002 PHE A 27 TRP 0.002 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 2829) covalent geometry : angle 0.60029 ( 3837) hydrogen bonds : bond 0.04045 ( 230) hydrogen bonds : angle 4.12305 ( 690) *********************** 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 88 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8480 (mm) cc_final: 0.8252 (mp) REVERT: A 131 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8121 (mpp) REVERT: A 156 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8345 (mttp) REVERT: A 209 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7802 (mp) REVERT: A 237 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 268 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 322 THR cc_start: 0.8588 (m) cc_final: 0.8342 (t) REVERT: A 340 MET cc_start: 0.8066 (mpt) cc_final: 0.7693 (mtm) REVERT: A 343 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7382 (mpt) outliers start: 12 outliers final: 4 residues processed: 82 average time/residue: 0.5175 time to fit residues: 43.4094 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 : 0.096 ------------------------------------------------------------------------------- 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 202 LEU Chi-restraints excluded: chain A residue 209 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 overall best weight: 0.2590 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.107987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095632 restraints weight = 4438.490| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.62 r_work: 0.3210 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2829 Z= 0.139 Angle : 0.644 8.355 3837 Z= 0.311 Chirality : 0.041 0.155 493 Planarity : 0.004 0.039 458 Dihedral : 3.989 19.427 383 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 4.30 % Allowed : 27.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.44), residues: 363 helix: 1.79 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.90 (1.10), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.020 0.002 TYR A 75 PHE 0.018 0.001 PHE A 27 TRP 0.001 0.000 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2829) covalent geometry : angle 0.64424 ( 3837) hydrogen bonds : bond 0.03931 ( 230) hydrogen bonds : angle 4.10247 ( 690) *********************** 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 89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8479 (mm) cc_final: 0.8241 (mp) REVERT: A 131 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8113 (mpp) REVERT: A 156 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8320 (mttp) REVERT: A 209 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7776 (mp) REVERT: A 210 LEU cc_start: 0.8290 (tt) cc_final: 0.7781 (tp) REVERT: A 237 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (tt) REVERT: A 268 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 322 THR cc_start: 0.8557 (m) cc_final: 0.8152 (m) REVERT: A 340 MET cc_start: 0.8084 (mpt) cc_final: 0.7738 (mtm) REVERT: A 343 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7370 (mpt) outliers start: 13 outliers final: 4 residues processed: 82 average time/residue: 0.5031 time to fit residues: 42.2740 Evaluate side-chains 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.0670 chunk 31 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.107599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095215 restraints weight = 4399.829| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.62 r_work: 0.3205 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2911 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= 0.146 Angle : 0.646 7.875 3837 Z= 0.312 Chirality : 0.041 0.157 493 Planarity : 0.004 0.038 458 Dihedral : 4.038 19.399 383 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.31 % Allowed : 29.14 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.44), residues: 363 helix: 1.73 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.82 (1.08), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.023 0.002 TYR A 75 PHE 0.019 0.002 PHE A 27 TRP 0.001 0.001 TRP A 192 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 2829) covalent geometry : angle 0.64603 ( 3837) hydrogen bonds : bond 0.04036 ( 230) hydrogen bonds : angle 4.14017 ( 690) ********************** 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 85 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8486 (mm) cc_final: 0.8246 (mp) REVERT: A 131 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8119 (mpp) REVERT: A 156 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8378 (mttp) REVERT: A 209 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 210 LEU cc_start: 0.8298 (tt) cc_final: 0.7781 (tp) REVERT: A 237 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 268 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 287 ILE cc_start: 0.8224 (mt) cc_final: 0.7946 (mt) REVERT: A 322 THR cc_start: 0.8550 (m) cc_final: 0.8168 (m) REVERT: A 340 MET cc_start: 0.8026 (mpt) cc_final: 0.7771 (mtm) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.4712 time to fit residues: 38.6009 Evaluate side-chains 86 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 28 ILE 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 3 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 0.2980 overall best weight: 0.1476 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.109769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097459 restraints weight = 4356.923| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.59 r_work: 0.3242 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2829 Z= 0.127 Angle : 0.635 8.216 3837 Z= 0.302 Chirality : 0.040 0.155 493 Planarity : 0.004 0.039 458 Dihedral : 3.952 19.373 383 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.98 % Allowed : 29.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.44), residues: 363 helix: 1.66 (0.29), residues: 327 sheet: None (None), residues: 0 loop : 0.55 (1.15), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 229 TYR 0.022 0.002 TYR A 75 PHE 0.019 0.001 PHE A 27 TRP 0.001 0.000 TRP A 192 HIS 0.000 0.000 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2829) covalent geometry : angle 0.63476 ( 3837) hydrogen bonds : bond 0.03711 ( 230) hydrogen bonds : angle 4.03131 ( 690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.63 seconds wall clock time: 23 minutes 23.43 seconds (1403.43 seconds total)