Starting phenix.real_space_refine on Tue Mar 3 12:42:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ski_10225/03_2026/6ski_10225.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ski_10225/03_2026/6ski_10225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ski_10225/03_2026/6ski_10225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ski_10225/03_2026/6ski_10225.map" model { file = "/net/cci-nas-00/data/ceres_data/6ski_10225/03_2026/6ski_10225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ski_10225/03_2026/6ski_10225.cif" } resolution = 2.6 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= -0.000 sd= 1.000 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 19 5.16 5 C 2818 2.51 5 N 776 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4434 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4092 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 498} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 342 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 1.16, per 1000 atoms: 0.26 Number of scatterers: 4434 At special positions: 0 Unit cell: (65.536, 71.68, 124.928, 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 19 16.00 O 821 8.00 N 776 7.00 C 2818 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: 0.33 Conformation dependent library (CDL) restraints added in 188.3 milliseconds 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 8 sheets defined 32.5% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'F' and resid 52 through 59 Processing helix chain 'F' and resid 71 through 86 Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 144 through 155 removed outlier: 4.149A pdb=" N THR F 148 " --> pdb=" O MET F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.580A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 348 Processing helix chain 'F' and resid 349 through 363 Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 388 through 395 Processing helix chain 'F' and resid 415 through 432 removed outlier: 3.771A pdb=" N VAL F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 451 through 467 Processing helix chain 'F' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.726A pdb=" N ILE F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 4 through 9 removed outlier: 4.316A pdb=" N TYR F 4 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE F 184 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG F 33 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE F 186 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL F 35 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 188 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 12.031A pdb=" N VAL F 238 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N ILE F 189 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N PHE F 240 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE F 191 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY F 242 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 193 " --> pdb=" O GLY F 242 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N LYS F 278 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG F 239 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE F 280 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU F 241 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 282 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU F 243 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA F 284 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU F 304 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN F 281 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU F 306 " --> pdb=" O GLN F 281 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR F 283 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 121 through 128 Processing sheet with id=AA3, first strand: chain 'F' and resid 294 through 296 removed outlier: 6.612A pdb=" N LEU F 294 " --> pdb=" O TRP F 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 328 through 331 Processing sheet with id=AA5, first strand: chain 'F' and resid 328 through 331 removed outlier: 4.568A pdb=" N GLN F 398 " --> pdb=" O VAL F 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 495 through 497 Processing sheet with id=AA7, first strand: chain 'F' and resid 500 through 502 Processing sheet with id=AA8, first strand: chain 'A' and resid 806 through 809 184 hydrogen bonds defined for protein. 516 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: 0.71 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1472 1.34 - 1.46: 874 1.46 - 1.57: 2150 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4528 Sorted by residual: bond pdb=" C LYS F 29 " pdb=" N LYS F 30 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 4.01e+00 bond pdb=" CA ARG F 198 " pdb=" C ARG F 198 " ideal model delta sigma weight residual 1.521 1.499 0.021 1.27e-02 6.20e+03 2.86e+00 bond pdb=" N GLY F 199 " pdb=" CA GLY F 199 " ideal model delta sigma weight residual 1.447 1.423 0.024 1.58e-02 4.01e+03 2.35e+00 bond pdb=" CA ASP F 245 " pdb=" C ASP F 245 " ideal model delta sigma weight residual 1.533 1.519 0.014 9.60e-03 1.09e+04 2.08e+00 bond pdb=" C SER F 197 " pdb=" N ARG F 198 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.42e-02 4.96e+03 1.72e+00 ... (remaining 4523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 6001 2.13 - 4.26: 106 4.26 - 6.40: 7 6.40 - 8.53: 3 8.53 - 10.66: 2 Bond angle restraints: 6119 Sorted by residual: angle pdb=" C PHE F 196 " pdb=" N SER F 197 " pdb=" CA SER F 197 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.12e+01 angle pdb=" N ARG F 198 " pdb=" CA ARG F 198 " pdb=" C ARG F 198 " ideal model delta sigma weight residual 113.97 109.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" N SER F 197 " pdb=" CA SER F 197 " pdb=" C SER F 197 " ideal model delta sigma weight residual 110.80 117.52 -6.72 2.13e+00 2.20e-01 9.95e+00 angle pdb=" C GLY F 199 " pdb=" N ALA F 200 " pdb=" CA ALA F 200 " ideal model delta sigma weight residual 121.80 115.35 6.45 2.16e+00 2.14e-01 8.93e+00 angle pdb=" C SER F 197 " pdb=" N ARG F 198 " pdb=" CA ARG F 198 " ideal model delta sigma weight residual 122.11 117.72 4.39 1.64e+00 3.72e-01 7.16e+00 ... (remaining 6114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2317 16.88 - 33.75: 278 33.75 - 50.63: 83 50.63 - 67.51: 17 67.51 - 84.38: 2 Dihedral angle restraints: 2697 sinusoidal: 1080 harmonic: 1617 Sorted by residual: dihedral pdb=" CA ARG F 198 " pdb=" C ARG F 198 " pdb=" N GLY F 199 " pdb=" CA GLY F 199 " ideal model delta harmonic sigma weight residual 180.00 147.70 32.30 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA LEU F 294 " pdb=" C LEU F 294 " pdb=" N ASN F 295 " pdb=" CA ASN F 295 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER F 329 " pdb=" C SER F 329 " pdb=" N LEU F 330 " pdb=" CA LEU F 330 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 2694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 393 0.033 - 0.066: 194 0.066 - 0.099: 53 0.099 - 0.132: 24 0.132 - 0.165: 1 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA PRO A 792 " pdb=" N PRO A 792 " pdb=" C PRO A 792 " pdb=" CB PRO A 792 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE A 809 " pdb=" N ILE A 809 " pdb=" C ILE A 809 " pdb=" CB ILE A 809 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA PRO F 273 " pdb=" N PRO F 273 " pdb=" C PRO F 273 " pdb=" CB PRO F 273 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 662 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 197 " -0.028 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C SER F 197 " 0.096 2.00e-02 2.50e+03 pdb=" O SER F 197 " -0.035 2.00e-02 2.50e+03 pdb=" N ARG F 198 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 204 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C ARG F 204 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG F 204 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS F 205 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 200 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ALA F 200 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA F 200 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA F 201 " 0.010 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 577 2.75 - 3.29: 4159 3.29 - 3.82: 7966 3.82 - 4.36: 9931 4.36 - 4.90: 16178 Nonbonded interactions: 38811 Sorted by model distance: nonbonded pdb=" NH2 ARG F 422 " pdb=" O LEU F 445 " model vdw 2.210 3.120 nonbonded pdb=" OD2 ASP F 44 " pdb=" OH TYR F 127 " model vdw 2.270 3.040 nonbonded pdb=" O SER F 181 " pdb=" OG SER F 181 " model vdw 2.285 3.040 nonbonded pdb=" O SER F 274 " pdb=" OG SER F 274 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP F 192 " pdb=" NH2 ARG F 239 " model vdw 2.303 3.120 ... (remaining 38806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.140 Find NCS groups from input model: 0.020 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:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.004 0.041 4528 Z= 0.218 Angle : 0.723 10.660 6119 Z= 0.408 Chirality : 0.043 0.165 665 Planarity : 0.005 0.056 800 Dihedral : 16.205 84.384 1659 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.29 % Allowed : 18.06 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -0.80 (0.33), residues: 557 helix: -0.58 (0.35), residues: 169 sheet: 0.20 (0.44), residues: 116 loop : -0.72 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 96 TYR 0.013 0.002 TYR F 230 PHE 0.021 0.002 PHE F 43 TRP 0.006 0.001 TRP F 501 HIS 0.005 0.002 HIS F 310 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 4528) covalent geometry : angle 0.72315 ( 6119) hydrogen bonds : bond 0.16695 ( 180) hydrogen bonds : angle 7.28948 ( 516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.173 Fit side-chains REVERT: F 49 ASN cc_start: 0.8735 (m110) cc_final: 0.8491 (m-40) REVERT: F 50 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7785 (mtt90) REVERT: F 83 LYS cc_start: 0.8556 (mttp) cc_final: 0.8168 (mtpt) REVERT: F 170 GLN cc_start: 0.7913 (tt0) cc_final: 0.7681 (tt0) REVERT: F 397 ILE cc_start: 0.9065 (mm) cc_final: 0.8821 (mm) REVERT: F 453 PHE cc_start: 0.7531 (t80) cc_final: 0.7271 (m-10) REVERT: F 520 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8477 (mtpt) REVERT: A 830 GLU cc_start: 0.7558 (mp0) cc_final: 0.7291 (mp0) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.6228 time to fit residues: 59.8463 Evaluate side-chains 72 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 HIS F 76 GLN F 106 ASN F 110 HIS F 123 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 213 GLN F 281 GLN F 286 ASN F 295 ASN F 387 ASN F 487 HIS F 493 ASN F 512 HIS A 791 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098905 restraints weight = 5386.843| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.68 r_work: 0.3170 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4528 Z= 0.182 Angle : 0.619 9.761 6119 Z= 0.323 Chirality : 0.043 0.160 665 Planarity : 0.004 0.050 800 Dihedral : 5.345 30.482 612 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.58 % Allowed : 19.78 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.06 (0.35), residues: 557 helix: 0.69 (0.38), residues: 165 sheet: 0.67 (0.51), residues: 93 loop : -0.48 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 33 TYR 0.010 0.002 TYR F 7 PHE 0.023 0.001 PHE F 43 TRP 0.005 0.001 TRP F 22 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4528) covalent geometry : angle 0.61853 ( 6119) hydrogen bonds : bond 0.04995 ( 180) hydrogen bonds : angle 5.54768 ( 516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.172 Fit side-chains REVERT: F 49 ASN cc_start: 0.8994 (m110) cc_final: 0.8732 (m-40) REVERT: F 83 LYS cc_start: 0.8701 (mttp) cc_final: 0.8267 (mtpt) REVERT: F 116 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8353 (mmtm) REVERT: F 303 GLU cc_start: 0.8634 (tt0) cc_final: 0.7977 (tt0) REVERT: F 357 GLN cc_start: 0.8088 (tt0) cc_final: 0.7575 (tm-30) REVERT: F 397 ILE cc_start: 0.9049 (mm) cc_final: 0.8792 (mm) REVERT: F 453 PHE cc_start: 0.7870 (t80) cc_final: 0.7510 (m-10) REVERT: F 513 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8222 (mtm-85) REVERT: F 520 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8645 (mtpt) REVERT: A 782 ILE cc_start: 0.6666 (mt) cc_final: 0.6466 (mt) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 0.6038 time to fit residues: 51.2397 Evaluate side-chains 76 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097279 restraints weight = 5439.338| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.68 r_work: 0.3144 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4528 Z= 0.239 Angle : 0.620 9.745 6119 Z= 0.328 Chirality : 0.044 0.155 665 Planarity : 0.004 0.052 800 Dihedral : 5.294 33.158 609 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.87 % Allowed : 19.57 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.15 (0.35), residues: 557 helix: 0.77 (0.38), residues: 166 sheet: 0.42 (0.49), residues: 93 loop : -0.32 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 272 TYR 0.010 0.002 TYR F 7 PHE 0.020 0.002 PHE F 43 TRP 0.009 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 4528) covalent geometry : angle 0.62041 ( 6119) hydrogen bonds : bond 0.05137 ( 180) hydrogen bonds : angle 5.50955 ( 516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.190 Fit side-chains REVERT: F 50 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7908 (mtt90) REVERT: F 83 LYS cc_start: 0.8715 (mttp) cc_final: 0.8296 (mtpt) REVERT: F 116 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8391 (mmtm) REVERT: F 303 GLU cc_start: 0.8677 (tt0) cc_final: 0.8100 (tt0) REVERT: F 357 GLN cc_start: 0.8132 (tt0) cc_final: 0.7619 (tm-30) REVERT: F 397 ILE cc_start: 0.9013 (mm) cc_final: 0.8756 (mm) REVERT: F 453 PHE cc_start: 0.7877 (t80) cc_final: 0.7553 (m-10) REVERT: F 520 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8654 (mtpt) REVERT: A 805 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7618 (mm) outliers start: 18 outliers final: 8 residues processed: 82 average time/residue: 0.5801 time to fit residues: 49.3919 Evaluate side-chains 75 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain A residue 805 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100454 restraints weight = 5396.885| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.69 r_work: 0.3182 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4528 Z= 0.139 Angle : 0.542 9.618 6119 Z= 0.286 Chirality : 0.042 0.141 665 Planarity : 0.004 0.048 800 Dihedral : 4.912 34.537 609 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.37 % Allowed : 21.51 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.38 (0.35), residues: 557 helix: 1.18 (0.39), residues: 166 sheet: 0.42 (0.49), residues: 93 loop : -0.27 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 272 TYR 0.008 0.001 TYR F 480 PHE 0.019 0.001 PHE F 43 TRP 0.006 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4528) covalent geometry : angle 0.54203 ( 6119) hydrogen bonds : bond 0.04309 ( 180) hydrogen bonds : angle 5.29382 ( 516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.133 Fit side-chains REVERT: F 49 ASN cc_start: 0.9030 (m110) cc_final: 0.8778 (m-40) REVERT: F 83 LYS cc_start: 0.8757 (mttp) cc_final: 0.8341 (mtpt) REVERT: F 116 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8320 (mmtm) REVERT: F 270 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: F 303 GLU cc_start: 0.8485 (tt0) cc_final: 0.7952 (tt0) REVERT: F 357 GLN cc_start: 0.8101 (tt0) cc_final: 0.7615 (tm-30) REVERT: F 453 PHE cc_start: 0.7921 (t80) cc_final: 0.7598 (m-10) REVERT: F 520 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8663 (mtpt) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.6681 time to fit residues: 52.3714 Evaluate side-chains 71 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 449 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.0010 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102683 restraints weight = 5376.663| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.70 r_work: 0.3214 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4528 Z= 0.114 Angle : 0.511 9.415 6119 Z= 0.269 Chirality : 0.041 0.136 665 Planarity : 0.004 0.047 800 Dihedral : 4.653 35.555 609 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.51 % Allowed : 22.37 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.50 (0.35), residues: 557 helix: 1.50 (0.39), residues: 166 sheet: 0.08 (0.46), residues: 113 loop : -0.20 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 272 TYR 0.008 0.001 TYR F 480 PHE 0.019 0.001 PHE F 43 TRP 0.005 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 4528) covalent geometry : angle 0.51116 ( 6119) hydrogen bonds : bond 0.03952 ( 180) hydrogen bonds : angle 5.10481 ( 516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.215 Fit side-chains REVERT: F 14 HIS cc_start: 0.6678 (t-170) cc_final: 0.6464 (t70) REVERT: F 49 ASN cc_start: 0.9005 (m110) cc_final: 0.8758 (m-40) REVERT: F 83 LYS cc_start: 0.8770 (mttp) cc_final: 0.8338 (mtpt) REVERT: F 116 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8326 (mmtm) REVERT: F 300 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6386 (tpt) REVERT: F 303 GLU cc_start: 0.8374 (tt0) cc_final: 0.7940 (tt0) REVERT: F 357 GLN cc_start: 0.8123 (tt0) cc_final: 0.7611 (tm-30) REVERT: F 453 PHE cc_start: 0.7900 (t80) cc_final: 0.7561 (m-10) REVERT: F 472 GLN cc_start: 0.8488 (tp40) cc_final: 0.8279 (tp40) REVERT: F 520 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8667 (mtpt) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.6635 time to fit residues: 48.6885 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 300 MET Chi-restraints excluded: chain A residue 805 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.0170 chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101247 restraints weight = 5472.337| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.69 r_work: 0.3196 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4528 Z= 0.136 Angle : 0.525 9.458 6119 Z= 0.277 Chirality : 0.042 0.134 665 Planarity : 0.004 0.048 800 Dihedral : 4.707 35.649 609 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.15 % Allowed : 23.23 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.60 (0.35), residues: 557 helix: 1.59 (0.39), residues: 166 sheet: 0.10 (0.46), residues: 111 loop : -0.12 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 272 TYR 0.008 0.001 TYR F 480 PHE 0.017 0.001 PHE F 43 TRP 0.008 0.001 TRP F 416 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4528) covalent geometry : angle 0.52539 ( 6119) hydrogen bonds : bond 0.04136 ( 180) hydrogen bonds : angle 5.11382 ( 516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: F 14 HIS cc_start: 0.6693 (t-170) cc_final: 0.6490 (t70) REVERT: F 49 ASN cc_start: 0.9001 (m110) cc_final: 0.8746 (m-40) REVERT: F 83 LYS cc_start: 0.8761 (mttp) cc_final: 0.8333 (mtpt) REVERT: F 116 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8361 (mmtm) REVERT: F 270 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: F 357 GLN cc_start: 0.8118 (tt0) cc_final: 0.7634 (tm-30) REVERT: F 453 PHE cc_start: 0.7905 (t80) cc_final: 0.7570 (m-10) REVERT: F 472 GLN cc_start: 0.8547 (tp40) cc_final: 0.8326 (tp40) REVERT: F 520 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8665 (mtpt) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 0.6063 time to fit residues: 43.9345 Evaluate side-chains 70 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 300 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN A 791 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100120 restraints weight = 5423.820| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.67 r_work: 0.3180 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4528 Z= 0.152 Angle : 0.538 9.501 6119 Z= 0.285 Chirality : 0.042 0.137 665 Planarity : 0.004 0.048 800 Dihedral : 4.769 35.724 609 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.15 % Allowed : 23.23 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.58 (0.35), residues: 557 helix: 1.60 (0.39), residues: 166 sheet: -0.05 (0.45), residues: 115 loop : -0.09 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 272 TYR 0.009 0.001 TYR F 109 PHE 0.019 0.001 PHE F 43 TRP 0.008 0.001 TRP F 416 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4528) covalent geometry : angle 0.53782 ( 6119) hydrogen bonds : bond 0.04297 ( 180) hydrogen bonds : angle 5.16625 ( 516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: F 14 HIS cc_start: 0.6593 (t-170) cc_final: 0.6304 (t-170) REVERT: F 49 ASN cc_start: 0.9012 (m110) cc_final: 0.8756 (m-40) REVERT: F 83 LYS cc_start: 0.8759 (mttp) cc_final: 0.8334 (mtpt) REVERT: F 116 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8355 (mmtm) REVERT: F 270 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: F 357 GLN cc_start: 0.8126 (tt0) cc_final: 0.7662 (tm-30) REVERT: F 453 PHE cc_start: 0.7889 (t80) cc_final: 0.7551 (m-10) REVERT: F 472 GLN cc_start: 0.8541 (tp40) cc_final: 0.8324 (tp40) REVERT: F 520 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8644 (mtpt) REVERT: A 830 GLU cc_start: 0.7819 (mp0) cc_final: 0.7584 (mp0) outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.6257 time to fit residues: 44.0431 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099581 restraints weight = 5405.386| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.68 r_work: 0.3179 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4528 Z= 0.164 Angle : 0.534 9.518 6119 Z= 0.287 Chirality : 0.042 0.140 665 Planarity : 0.004 0.049 800 Dihedral : 4.819 35.611 609 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.58 % Allowed : 23.01 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.53 (0.35), residues: 557 helix: 1.56 (0.39), residues: 166 sheet: -0.08 (0.46), residues: 115 loop : -0.11 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 272 TYR 0.010 0.001 TYR F 109 PHE 0.018 0.001 PHE F 43 TRP 0.009 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4528) covalent geometry : angle 0.53423 ( 6119) hydrogen bonds : bond 0.04395 ( 180) hydrogen bonds : angle 5.21366 ( 516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: F 14 HIS cc_start: 0.6630 (t-170) cc_final: 0.6319 (t-170) REVERT: F 83 LYS cc_start: 0.8752 (mttp) cc_final: 0.8332 (mtpt) REVERT: F 116 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8352 (mmtm) REVERT: F 270 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: F 357 GLN cc_start: 0.8130 (tt0) cc_final: 0.7654 (tm-30) REVERT: F 453 PHE cc_start: 0.7897 (t80) cc_final: 0.7552 (m-10) REVERT: F 472 GLN cc_start: 0.8575 (tp40) cc_final: 0.8354 (tp40) REVERT: F 520 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8645 (mtpt) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 0.6498 time to fit residues: 43.6558 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097845 restraints weight = 5451.909| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.68 r_work: 0.3153 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4528 Z= 0.205 Angle : 0.560 9.578 6119 Z= 0.302 Chirality : 0.043 0.147 665 Planarity : 0.004 0.050 800 Dihedral : 4.983 35.638 609 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 23.23 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.41 (0.35), residues: 557 helix: 1.45 (0.38), residues: 166 sheet: -0.11 (0.46), residues: 117 loop : -0.20 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 272 TYR 0.012 0.002 TYR F 109 PHE 0.018 0.001 PHE F 43 TRP 0.010 0.001 TRP F 416 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 4528) covalent geometry : angle 0.55985 ( 6119) hydrogen bonds : bond 0.04698 ( 180) hydrogen bonds : angle 5.30874 ( 516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: F 83 LYS cc_start: 0.8750 (mttp) cc_final: 0.8330 (mtpt) REVERT: F 116 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8382 (mmtm) REVERT: F 117 LYS cc_start: 0.8526 (mttt) cc_final: 0.8163 (mtmm) REVERT: F 183 ASP cc_start: 0.8330 (t0) cc_final: 0.8070 (t0) REVERT: F 270 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: F 357 GLN cc_start: 0.8151 (tt0) cc_final: 0.7640 (tm-30) REVERT: F 453 PHE cc_start: 0.7912 (t80) cc_final: 0.7542 (m-10) REVERT: F 472 GLN cc_start: 0.8561 (tp40) cc_final: 0.8334 (tp40) REVERT: F 520 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8630 (mtpt) REVERT: A 830 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7631 (mp0) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.6013 time to fit residues: 41.0264 Evaluate side-chains 71 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 830 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099973 restraints weight = 5413.715| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.66 r_work: 0.3180 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4528 Z= 0.153 Angle : 0.544 9.560 6119 Z= 0.290 Chirality : 0.042 0.139 665 Planarity : 0.004 0.048 800 Dihedral : 4.810 35.711 609 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.94 % Allowed : 23.44 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.53 (0.35), residues: 557 helix: 1.60 (0.39), residues: 166 sheet: 0.39 (0.51), residues: 96 loop : -0.34 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 272 TYR 0.008 0.001 TYR F 109 PHE 0.019 0.001 PHE F 43 TRP 0.007 0.001 TRP F 416 HIS 0.006 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4528) covalent geometry : angle 0.54354 ( 6119) hydrogen bonds : bond 0.04313 ( 180) hydrogen bonds : angle 5.24664 ( 516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: F 83 LYS cc_start: 0.8764 (mttp) cc_final: 0.8339 (mtpt) REVERT: F 116 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8332 (mmtm) REVERT: F 183 ASP cc_start: 0.8262 (t0) cc_final: 0.8003 (t0) REVERT: F 270 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: F 290 TYR cc_start: 0.9127 (t80) cc_final: 0.8844 (t80) REVERT: F 357 GLN cc_start: 0.8153 (tt0) cc_final: 0.7655 (tm-30) REVERT: F 453 PHE cc_start: 0.7893 (t80) cc_final: 0.7548 (m-10) REVERT: F 472 GLN cc_start: 0.8547 (tp40) cc_final: 0.8333 (tp40) REVERT: F 520 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8654 (mtpt) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.5845 time to fit residues: 39.8611 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 36 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099867 restraints weight = 5431.597| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.67 r_work: 0.3179 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4528 Z= 0.155 Angle : 0.533 9.506 6119 Z= 0.288 Chirality : 0.042 0.139 665 Planarity : 0.004 0.048 800 Dihedral : 4.787 35.653 609 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.94 % Allowed : 23.66 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: 0.59 (0.35), residues: 557 helix: 1.63 (0.39), residues: 166 sheet: 0.37 (0.51), residues: 94 loop : -0.27 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 272 TYR 0.009 0.001 TYR F 109 PHE 0.018 0.001 PHE F 43 TRP 0.007 0.001 TRP F 416 HIS 0.007 0.001 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4528) covalent geometry : angle 0.53342 ( 6119) hydrogen bonds : bond 0.04309 ( 180) hydrogen bonds : angle 5.24519 ( 516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.99 seconds wall clock time: 32 minutes 49.69 seconds (1969.69 seconds total)