Starting phenix.real_space_refine on Tue Feb 11 08:15:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y56_38930/02_2025/8y56_38930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y56_38930/02_2025/8y56_38930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y56_38930/02_2025/8y56_38930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y56_38930/02_2025/8y56_38930.map" model { file = "/net/cci-nas-00/data/ceres_data/8y56_38930/02_2025/8y56_38930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y56_38930/02_2025/8y56_38930.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 Na 1 4.78 5 C 3252 2.51 5 N 718 2.21 5 O 796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4796 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4601 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 22, 'TRANS': 563} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 195 Unusual residues: {' NA': 1, 'CLR': 5, 'DKB': 1} Classifications: {'undetermined': 7, 'water': 5} Link IDs: {None: 11} Time building chain proxies: 3.44, per 1000 atoms: 0.72 Number of scatterers: 4796 At special positions: 0 Unit cell: (72.54, 63.24, 96.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 1 15.00 Na 1 11.00 O 796 8.00 N 718 7.00 C 3252 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: 1.26 Conformation dependent library (CDL) restraints added in 572.4 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1096 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'R' and resid 38 through 40 No H-bonds generated for 'chain 'R' and resid 38 through 40' Processing helix chain 'R' and resid 41 through 62 Processing helix chain 'R' and resid 66 through 80 removed outlier: 3.575A pdb=" N PHE R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 92 removed outlier: 3.828A pdb=" N VAL R 92 " --> pdb=" O LYS R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 98 removed outlier: 3.505A pdb=" N ASN R 97 " --> pdb=" O ASN R 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL R 98 " --> pdb=" O PHE R 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 94 through 98' Processing helix chain 'R' and resid 99 through 124 removed outlier: 4.035A pdb=" N LEU R 103 " --> pdb=" O ASP R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 128 No H-bonds generated for 'chain 'R' and resid 126 through 128' Processing helix chain 'R' and resid 129 through 143 removed outlier: 3.746A pdb=" N LYS R 133 " --> pdb=" O SER R 129 " (cutoff:3.500A) Proline residue: R 138 - end of helix Processing helix chain 'R' and resid 149 through 158 removed outlier: 3.889A pdb=" N ILE R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 196 removed outlier: 4.041A pdb=" N TYR R 168 " --> pdb=" O GLU R 164 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE R 169 " --> pdb=" O TYR R 165 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU R 171 " --> pdb=" O GLN R 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) Proline residue: R 174 - end of helix Proline residue: R 182 - end of helix Processing helix chain 'R' and resid 197 through 201 Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.725A pdb=" N VAL R 214 " --> pdb=" O GLY R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 233 removed outlier: 3.540A pdb=" N PHE R 221 " --> pdb=" O ASN R 217 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL R 223 " --> pdb=" O ILE R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 250 Processing helix chain 'R' and resid 251 through 264 removed outlier: 3.590A pdb=" N SER R 255 " --> pdb=" O SER R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 288 Processing helix chain 'R' and resid 288 through 302 removed outlier: 3.562A pdb=" N LEU R 300 " --> pdb=" O GLU R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 322 Processing helix chain 'R' and resid 326 through 337 removed outlier: 4.290A pdb=" N ALA R 330 " --> pdb=" O ALA R 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE R 331 " --> pdb=" O PRO R 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 367 removed outlier: 3.996A pdb=" N ALA R 355 " --> pdb=" O THR R 351 " (cutoff:3.500A) Proline residue: R 356 - end of helix removed outlier: 3.620A pdb=" N THR R 366 " --> pdb=" O ALA R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 370 No H-bonds generated for 'chain 'R' and resid 368 through 370' Processing helix chain 'R' and resid 371 through 404 removed outlier: 3.551A pdb=" N VAL R 389 " --> pdb=" O ASP R 385 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER R 404 " --> pdb=" O ILE R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 408 Processing helix chain 'R' and resid 409 through 436 removed outlier: 3.687A pdb=" N LEU R 414 " --> pdb=" O LEU R 410 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE R 434 " --> pdb=" O MET R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 439 through 474 removed outlier: 3.515A pdb=" N LEU R 445 " --> pdb=" O VAL R 441 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 453 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY R 462 " --> pdb=" O TYR R 458 " (cutoff:3.500A) Processing helix chain 'R' and resid 480 through 502 Proline residue: R 492 - end of helix Processing helix chain 'R' and resid 517 through 546 removed outlier: 3.882A pdb=" N MET R 521 " --> pdb=" O GLY R 517 " (cutoff:3.500A) Processing helix chain 'R' and resid 654 through 682 Processing helix chain 'R' and resid 688 through 711 removed outlier: 3.564A pdb=" N PHE R 701 " --> pdb=" O ALA R 697 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY R 704 " --> pdb=" O ASN R 700 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE R 705 " --> pdb=" O PHE R 701 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE R 710 " --> pdb=" O ILE R 706 " (cutoff:3.500A) Processing helix chain 'R' and resid 719 through 724 355 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 691 1.30 - 1.42: 1249 1.42 - 1.55: 2920 1.55 - 1.68: 10 1.68 - 1.81: 45 Bond restraints: 4915 Sorted by residual: bond pdb=" C39 DKB R 907 " pdb=" C40 DKB R 907 " ideal model delta sigma weight residual 1.526 1.294 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" CA GLY R 704 " pdb=" C GLY R 704 " ideal model delta sigma weight residual 1.516 1.448 0.068 1.12e-02 7.97e+03 3.74e+01 bond pdb=" CA ARG R 295 " pdb=" C ARG R 295 " ideal model delta sigma weight residual 1.522 1.448 0.074 1.37e-02 5.33e+03 2.91e+01 bond pdb=" CA PHE R 708 " pdb=" CB PHE R 708 " ideal model delta sigma weight residual 1.531 1.448 0.083 1.56e-02 4.11e+03 2.82e+01 bond pdb=" C ARG R 295 " pdb=" O ARG R 295 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.32e-02 5.74e+03 2.50e+01 ... (remaining 4910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 6552 2.14 - 4.28: 118 4.28 - 6.42: 21 6.42 - 8.57: 3 8.57 - 10.71: 2 Bond angle restraints: 6696 Sorted by residual: angle pdb=" C PHE R 705 " pdb=" N ILE R 706 " pdb=" CA ILE R 706 " ideal model delta sigma weight residual 120.46 112.31 8.15 1.37e+00 5.33e-01 3.54e+01 angle pdb=" N ILE R 706 " pdb=" CA ILE R 706 " pdb=" CB ILE R 706 " ideal model delta sigma weight residual 110.54 118.51 -7.97 1.36e+00 5.41e-01 3.43e+01 angle pdb=" CA ILE R 706 " pdb=" C ILE R 706 " pdb=" N SER R 707 " ideal model delta sigma weight residual 117.15 122.15 -5.00 1.14e+00 7.69e-01 1.93e+01 angle pdb=" N PHE R 705 " pdb=" CA PHE R 705 " pdb=" C PHE R 705 " ideal model delta sigma weight residual 111.36 106.61 4.75 1.09e+00 8.42e-01 1.90e+01 angle pdb=" N ILE R 706 " pdb=" CA ILE R 706 " pdb=" C ILE R 706 " ideal model delta sigma weight residual 110.62 114.88 -4.26 1.02e+00 9.61e-01 1.74e+01 ... (remaining 6691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 3049 35.00 - 70.00: 74 70.00 - 105.01: 11 105.01 - 140.01: 1 140.01 - 175.01: 1 Dihedral angle restraints: 3136 sinusoidal: 1436 harmonic: 1700 Sorted by residual: dihedral pdb=" C12 DKB R 907 " pdb=" C13 DKB R 907 " pdb=" C14 DKB R 907 " pdb=" C15 DKB R 907 " ideal model delta sinusoidal sigma weight residual -75.25 99.76 -175.01 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N ILE R 706 " pdb=" C ILE R 706 " pdb=" CA ILE R 706 " pdb=" CB ILE R 706 " ideal model delta harmonic sigma weight residual 123.40 134.81 -11.41 0 2.50e+00 1.60e-01 2.08e+01 dihedral pdb=" C PHE R 708 " pdb=" N PHE R 708 " pdb=" CA PHE R 708 " pdb=" CB PHE R 708 " ideal model delta harmonic sigma weight residual -122.60 -111.80 -10.80 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 3133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 717 0.064 - 0.128: 84 0.128 - 0.191: 4 0.191 - 0.255: 3 0.255 - 0.319: 1 Chirality restraints: 809 Sorted by residual: chirality pdb=" C13 CLR R 904 " pdb=" C12 CLR R 904 " pdb=" C14 CLR R 904 " pdb=" C17 CLR R 904 " both_signs ideal model delta sigma weight residual False -2.93 -2.61 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA ILE R 706 " pdb=" N ILE R 706 " pdb=" C ILE R 706 " pdb=" CB ILE R 706 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C10 CLR R 904 " pdb=" C1 CLR R 904 " pdb=" C5 CLR R 904 " pdb=" C9 CLR R 904 " both_signs ideal model delta sigma weight residual False -2.85 -2.63 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 806 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 708 " 0.026 2.00e-02 2.50e+03 2.02e-02 7.15e+00 pdb=" CG PHE R 708 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE R 708 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE R 708 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 708 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 708 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 708 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 294 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C CYS R 294 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS R 294 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG R 295 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 705 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PHE R 705 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE R 705 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE R 706 " 0.010 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1268 2.80 - 3.33: 5075 3.33 - 3.85: 7916 3.85 - 4.38: 9963 4.38 - 4.90: 16443 Nonbonded interactions: 40665 Sorted by model distance: nonbonded pdb=" O LEU R 85 " pdb=" ND2 ASN R 89 " model vdw 2.279 3.120 nonbonded pdb=" O SER R 390 " pdb=" OG SER R 393 " model vdw 2.312 3.040 nonbonded pdb=" OG SER R 144 " pdb=" OD1 ASP R 146 " model vdw 2.327 3.040 nonbonded pdb=" O PHE R 384 " pdb=" OG SER R 387 " model vdw 2.352 3.040 nonbonded pdb=" NZ LYS R 133 " pdb=" OE2 GLU R 339 " model vdw 2.355 3.120 ... (remaining 40660 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.006 0.232 4915 Z= 0.368 Angle : 0.727 10.706 6696 Z= 0.396 Chirality : 0.044 0.319 809 Planarity : 0.004 0.042 776 Dihedral : 15.556 175.010 2040 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.98 % Allowed : 0.78 % Favored : 98.24 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.34), residues: 582 helix: 1.04 (0.24), residues: 452 sheet: None (None), residues: 0 loop : -1.34 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 100 HIS 0.002 0.001 HIS R 658 PHE 0.046 0.001 PHE R 708 TYR 0.010 0.001 TYR R 451 ARG 0.002 0.000 ARG R 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.505 Fit side-chains REVERT: R 236 LYS cc_start: 0.7437 (mppt) cc_final: 0.7193 (mppt) REVERT: R 529 PHE cc_start: 0.8051 (t80) cc_final: 0.7821 (t80) outliers start: 5 outliers final: 1 residues processed: 94 average time/residue: 1.0767 time to fit residues: 105.9838 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 ASN R 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121987 restraints weight = 5341.896| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.92 r_work: 0.3309 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4915 Z= 0.267 Angle : 0.645 8.027 6696 Z= 0.321 Chirality : 0.043 0.146 809 Planarity : 0.005 0.046 776 Dihedral : 14.097 173.316 997 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.16 % Allowed : 9.61 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.35), residues: 582 helix: 1.75 (0.24), residues: 464 sheet: None (None), residues: 0 loop : -1.19 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 396 HIS 0.003 0.001 HIS R 310 PHE 0.030 0.002 PHE R 231 TYR 0.022 0.002 TYR R 451 ARG 0.002 0.000 ARG R 687 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.499 Fit side-chains REVERT: R 103 LEU cc_start: 0.8030 (tp) cc_final: 0.7552 (mm) REVERT: R 120 LEU cc_start: 0.7954 (mt) cc_final: 0.7736 (mt) REVERT: R 143 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: R 276 PHE cc_start: 0.6349 (t80) cc_final: 0.6085 (m-10) REVERT: R 301 LEU cc_start: 0.7678 (mm) cc_final: 0.7370 (mm) REVERT: R 413 MET cc_start: 0.6746 (ttm) cc_final: 0.6415 (ttm) REVERT: R 678 TRP cc_start: 0.6726 (t60) cc_final: 0.5994 (t60) outliers start: 11 outliers final: 3 residues processed: 79 average time/residue: 1.0100 time to fit residues: 83.6897 Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 705 PHE Chi-restraints excluded: chain R residue 713 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121975 restraints weight = 5388.948| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.89 r_work: 0.3298 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4915 Z= 0.252 Angle : 0.578 8.520 6696 Z= 0.289 Chirality : 0.042 0.144 809 Planarity : 0.005 0.047 776 Dihedral : 13.015 161.038 997 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.33 % Allowed : 11.18 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.34), residues: 582 helix: 1.91 (0.24), residues: 460 sheet: None (None), residues: 0 loop : -1.04 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 193 HIS 0.003 0.001 HIS R 310 PHE 0.024 0.002 PHE R 221 TYR 0.020 0.002 TYR R 451 ARG 0.003 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8077 (mt) cc_final: 0.7853 (mt) REVERT: R 143 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: R 146 ASP cc_start: 0.8619 (m-30) cc_final: 0.8389 (m-30) REVERT: R 236 LYS cc_start: 0.7118 (mppt) cc_final: 0.6875 (mtmm) REVERT: R 276 PHE cc_start: 0.6477 (t80) cc_final: 0.6083 (m-10) REVERT: R 280 ILE cc_start: 0.8023 (mt) cc_final: 0.7796 (mp) REVERT: R 301 LEU cc_start: 0.7830 (mm) cc_final: 0.7615 (mm) REVERT: R 302 ASP cc_start: 0.7550 (t70) cc_final: 0.7113 (t70) REVERT: R 303 LYS cc_start: 0.6841 (pptt) cc_final: 0.6599 (mmmt) REVERT: R 511 ASP cc_start: 0.7610 (t0) cc_final: 0.7398 (t0) REVERT: R 678 TRP cc_start: 0.6738 (t60) cc_final: 0.6107 (t60) outliers start: 17 outliers final: 6 residues processed: 89 average time/residue: 0.9370 time to fit residues: 87.6017 Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 713 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 0.0060 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.154848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124032 restraints weight = 5407.229| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.90 r_work: 0.3328 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4915 Z= 0.187 Angle : 0.552 9.313 6696 Z= 0.275 Chirality : 0.041 0.146 809 Planarity : 0.004 0.046 776 Dihedral : 12.264 149.216 997 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.94 % Allowed : 13.92 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.35), residues: 582 helix: 2.10 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.05 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 193 HIS 0.002 0.001 HIS R 310 PHE 0.020 0.001 PHE R 221 TYR 0.017 0.001 TYR R 451 ARG 0.004 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8144 (mt) cc_final: 0.7898 (mt) REVERT: R 143 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: R 216 GLN cc_start: 0.7752 (mt0) cc_final: 0.7498 (mt0) REVERT: R 235 ARG cc_start: 0.7275 (mtm-85) cc_final: 0.6535 (mtm-85) REVERT: R 236 LYS cc_start: 0.7190 (mppt) cc_final: 0.6930 (mppt) REVERT: R 246 ASP cc_start: 0.6778 (m-30) cc_final: 0.6313 (m-30) REVERT: R 276 PHE cc_start: 0.6435 (t80) cc_final: 0.6073 (m-10) REVERT: R 280 ILE cc_start: 0.7981 (mt) cc_final: 0.7759 (mp) REVERT: R 413 MET cc_start: 0.6770 (ttm) cc_final: 0.6442 (ttm) REVERT: R 511 ASP cc_start: 0.7596 (t0) cc_final: 0.7378 (t0) REVERT: R 678 TRP cc_start: 0.6682 (t60) cc_final: 0.6111 (t60) outliers start: 15 outliers final: 5 residues processed: 86 average time/residue: 0.9298 time to fit residues: 84.1147 Evaluate side-chains 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122348 restraints weight = 5458.906| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.92 r_work: 0.3329 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4915 Z= 0.225 Angle : 0.562 10.026 6696 Z= 0.279 Chirality : 0.041 0.144 809 Planarity : 0.004 0.047 776 Dihedral : 11.825 139.188 997 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.35 % Allowed : 14.71 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.35), residues: 582 helix: 2.15 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -1.21 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 193 HIS 0.003 0.001 HIS R 310 PHE 0.022 0.001 PHE R 221 TYR 0.013 0.001 TYR R 451 ARG 0.002 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8162 (mt) cc_final: 0.7924 (mt) REVERT: R 235 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.6617 (mtm-85) REVERT: R 236 LYS cc_start: 0.7172 (mppt) cc_final: 0.6922 (mppt) REVERT: R 276 PHE cc_start: 0.6510 (t80) cc_final: 0.6068 (m-10) REVERT: R 280 ILE cc_start: 0.7978 (mt) cc_final: 0.7760 (mp) REVERT: R 299 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7200 (mm-30) REVERT: R 413 MET cc_start: 0.6843 (ttm) cc_final: 0.6483 (ttm) REVERT: R 678 TRP cc_start: 0.6740 (t60) cc_final: 0.6181 (t60) outliers start: 12 outliers final: 5 residues processed: 75 average time/residue: 0.9774 time to fit residues: 76.9912 Evaluate side-chains 68 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122906 restraints weight = 5360.853| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.85 r_work: 0.3319 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4915 Z= 0.225 Angle : 0.576 10.768 6696 Z= 0.282 Chirality : 0.042 0.144 809 Planarity : 0.004 0.047 776 Dihedral : 11.403 128.207 997 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.55 % Allowed : 14.90 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.35), residues: 582 helix: 2.17 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -1.19 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 193 HIS 0.003 0.001 HIS R 310 PHE 0.023 0.001 PHE R 221 TYR 0.014 0.001 TYR R 451 ARG 0.002 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: R 93 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7590 (tt) REVERT: R 120 LEU cc_start: 0.8182 (mt) cc_final: 0.7965 (mt) REVERT: R 235 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.6664 (mtm-85) REVERT: R 236 LYS cc_start: 0.7154 (mppt) cc_final: 0.6882 (mtmm) REVERT: R 276 PHE cc_start: 0.6542 (t80) cc_final: 0.6087 (m-10) REVERT: R 280 ILE cc_start: 0.7959 (mt) cc_final: 0.7754 (mp) REVERT: R 299 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7223 (mm-30) REVERT: R 413 MET cc_start: 0.6827 (ttm) cc_final: 0.6469 (ttm) REVERT: R 678 TRP cc_start: 0.6714 (t60) cc_final: 0.6160 (t60) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 1.0147 time to fit residues: 80.9432 Evaluate side-chains 68 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121752 restraints weight = 5332.119| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.89 r_work: 0.3321 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4915 Z= 0.260 Angle : 0.602 11.457 6696 Z= 0.292 Chirality : 0.042 0.144 809 Planarity : 0.005 0.047 776 Dihedral : 11.249 123.717 997 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.35), residues: 582 helix: 2.10 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.18 (0.53), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 363 HIS 0.003 0.001 HIS R 310 PHE 0.023 0.002 PHE R 221 TYR 0.015 0.002 TYR R 451 ARG 0.002 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.490 Fit side-chains REVERT: R 120 LEU cc_start: 0.8148 (mt) cc_final: 0.7920 (mt) REVERT: R 235 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6658 (mtm-85) REVERT: R 276 PHE cc_start: 0.6556 (t80) cc_final: 0.6078 (m-10) REVERT: R 280 ILE cc_start: 0.7980 (mt) cc_final: 0.7775 (mp) REVERT: R 385 ASP cc_start: 0.8270 (p0) cc_final: 0.7959 (p0) REVERT: R 413 MET cc_start: 0.6742 (ttm) cc_final: 0.6360 (ttm) REVERT: R 678 TRP cc_start: 0.6748 (t60) cc_final: 0.6188 (t60) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.9679 time to fit residues: 76.3389 Evaluate side-chains 70 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 GLN ** R 310 HIS ** 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 = 0.3803 r_free = 0.3803 target = 0.155029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123949 restraints weight = 5391.682| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.90 r_work: 0.3337 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4915 Z= 0.190 Angle : 0.570 11.369 6696 Z= 0.276 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.970 121.146 997 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.57 % Allowed : 16.08 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.35), residues: 582 helix: 2.18 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -1.21 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 679 HIS 0.002 0.001 HIS R 310 PHE 0.021 0.001 PHE R 221 TYR 0.013 0.001 TYR R 451 ARG 0.002 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.544 Fit side-chains REVERT: R 41 ARG cc_start: 0.7606 (mtm180) cc_final: 0.6819 (mtm180) REVERT: R 120 LEU cc_start: 0.8142 (mt) cc_final: 0.7913 (mt) REVERT: R 234 ASP cc_start: 0.6200 (t70) cc_final: 0.5833 (t70) REVERT: R 235 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6475 (mtm-85) REVERT: R 236 LYS cc_start: 0.7222 (mppt) cc_final: 0.6980 (mppt) REVERT: R 246 ASP cc_start: 0.6712 (m-30) cc_final: 0.6326 (m-30) REVERT: R 276 PHE cc_start: 0.6572 (t80) cc_final: 0.6085 (m-10) REVERT: R 280 ILE cc_start: 0.7945 (mt) cc_final: 0.7735 (mp) REVERT: R 413 MET cc_start: 0.6709 (ttm) cc_final: 0.6329 (ttm) REVERT: R 511 ASP cc_start: 0.7685 (t0) cc_final: 0.7467 (t0) REVERT: R 678 TRP cc_start: 0.6688 (t60) cc_final: 0.6054 (t60) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.9094 time to fit residues: 80.8229 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123357 restraints weight = 5354.704| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.90 r_work: 0.3407 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4915 Z= 0.195 Angle : 0.563 11.871 6696 Z= 0.277 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.818 119.835 997 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.98 % Allowed : 16.67 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.35), residues: 582 helix: 2.23 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -1.28 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 363 HIS 0.002 0.001 HIS R 310 PHE 0.021 0.001 PHE R 221 TYR 0.014 0.001 TYR R 451 ARG 0.002 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.469 Fit side-chains REVERT: R 41 ARG cc_start: 0.7532 (mtm180) cc_final: 0.6816 (mtm180) REVERT: R 120 LEU cc_start: 0.8157 (mt) cc_final: 0.7922 (mt) REVERT: R 235 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6503 (mtm-85) REVERT: R 276 PHE cc_start: 0.6549 (t80) cc_final: 0.6052 (m-10) REVERT: R 280 ILE cc_start: 0.7892 (mt) cc_final: 0.7687 (mp) REVERT: R 413 MET cc_start: 0.6654 (ttm) cc_final: 0.6272 (ttm) REVERT: R 678 TRP cc_start: 0.6650 (t60) cc_final: 0.6050 (t60) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.9743 time to fit residues: 73.8791 Evaluate side-chains 68 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 GLN ** R 310 HIS ** 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 = 0.3805 r_free = 0.3805 target = 0.155426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125185 restraints weight = 5303.103| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.85 r_work: 0.3427 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4915 Z= 0.175 Angle : 0.563 11.916 6696 Z= 0.277 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.347 118.315 994 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.18 % Allowed : 16.67 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.35), residues: 582 helix: 2.33 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.21 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 363 HIS 0.002 0.001 HIS R 310 PHE 0.020 0.001 PHE R 221 TYR 0.013 0.001 TYR R 451 ARG 0.002 0.000 ARG R 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.509 Fit side-chains REVERT: R 41 ARG cc_start: 0.7472 (mtm180) cc_final: 0.6739 (mtm180) REVERT: R 120 LEU cc_start: 0.8144 (mt) cc_final: 0.7914 (mt) REVERT: R 235 ARG cc_start: 0.6999 (mtm-85) cc_final: 0.6455 (mtm-85) REVERT: R 276 PHE cc_start: 0.6543 (t80) cc_final: 0.6052 (m-10) REVERT: R 280 ILE cc_start: 0.7885 (mt) cc_final: 0.7676 (mp) REVERT: R 413 MET cc_start: 0.6645 (ttm) cc_final: 0.6272 (ttm) REVERT: R 678 TRP cc_start: 0.6627 (t60) cc_final: 0.5980 (t60) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.8836 time to fit residues: 74.6214 Evaluate side-chains 73 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 472 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122167 restraints weight = 5418.282| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.92 r_work: 0.3318 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4915 Z= 0.241 Angle : 0.577 9.932 6696 Z= 0.285 Chirality : 0.042 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.310 118.818 994 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.96 % Allowed : 16.27 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.35), residues: 582 helix: 2.24 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.21 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 363 HIS 0.002 0.001 HIS R 310 PHE 0.027 0.002 PHE R 529 TYR 0.015 0.001 TYR R 451 ARG 0.002 0.000 ARG R 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.97 seconds wall clock time: 61 minutes 38.05 seconds (3698.05 seconds total)