Starting phenix.real_space_refine on Thu Mar 6 04:04:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y56_38930/03_2025/8y56_38930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y56_38930/03_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_38930/03_2025/8y56_38930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y56_38930/03_2025/8y56_38930.map" model { file = "/net/cci-nas-00/data/ceres_data/8y56_38930/03_2025/8y56_38930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y56_38930/03_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-5624/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: 3.67, per 1000 atoms: 0.77 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: 1.20 Conformation dependent library (CDL) restraints added in 531.4 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: 0.40 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: 1.26 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.340 Find NCS groups from input model: 0.040 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- 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 : 0.451 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: 1.0621 time to fit residues: 104.6166 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 : 0.503 ------------------------------------------------------------------------------- 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: 4.48 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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: 0.8033 (tp) cc_final: 0.7555 (mm) REVERT: R 120 LEU cc_start: 0.7956 (mt) cc_final: 0.7739 (mt) REVERT: R 143 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: R 276 PHE cc_start: 0.6347 (t80) cc_final: 0.6083 (m-10) REVERT: R 301 LEU cc_start: 0.7679 (mm) cc_final: 0.7371 (mm) REVERT: R 413 MET cc_start: 0.6747 (ttm) cc_final: 0.6416 (ttm) REVERT: R 678 TRP cc_start: 0.6732 (t60) cc_final: 0.6000 (t60) outliers start: 11 outliers final: 3 residues processed: 79 average time/residue: 0.9759 time to fit residues: 80.9497 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 : 0.507 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 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 310 HIS ** 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 = 0.3783 r_free = 0.3783 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122266 restraints weight = 5384.399| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.89 r_work: 0.3323 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2172 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= 0.244 Angle : 0.577 8.889 6696 Z= 0.288 Chirality : 0.042 0.145 809 Planarity : 0.005 0.047 776 Dihedral : 13.062 162.071 997 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.53 % Allowed : 10.98 % 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: 1.97 (0.34), residues: 582 helix: 1.88 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -0.95 (0.56), residues: 120 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 0.002 PHE R 221 TYR 0.020 0.002 TYR R 451 ARG 0.002 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 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8089 (mt) cc_final: 0.7871 (mt) REVERT: R 143 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: R 146 ASP cc_start: 0.8622 (m-30) cc_final: 0.8394 (m-30) REVERT: R 227 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7502 (mp) REVERT: R 236 LYS cc_start: 0.7125 (mppt) cc_final: 0.6876 (mtmm) REVERT: R 276 PHE cc_start: 0.6478 (t80) cc_final: 0.6085 (m-10) REVERT: R 280 ILE cc_start: 0.8028 (mt) cc_final: 0.7800 (mp) REVERT: R 301 LEU cc_start: 0.7827 (mm) cc_final: 0.7575 (mm) REVERT: R 302 ASP cc_start: 0.7550 (t70) cc_final: 0.7112 (t70) REVERT: R 303 LYS cc_start: 0.6772 (pptt) cc_final: 0.6534 (mmmt) REVERT: R 511 ASP cc_start: 0.7617 (t0) cc_final: 0.7410 (t0) REVERT: R 678 TRP cc_start: 0.6746 (t60) cc_final: 0.6115 (t60) outliers start: 18 outliers final: 6 residues processed: 89 average time/residue: 0.9021 time to fit residues: 84.5348 Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 227 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: 0.6980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.152982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121927 restraints weight = 5413.709| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.90 r_work: 0.3345 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2407 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= 0.230 Angle : 0.573 9.516 6696 Z= 0.284 Chirality : 0.042 0.147 809 Planarity : 0.005 0.047 776 Dihedral : 12.474 150.694 997 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.94 % Allowed : 14.12 % 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: 2.05 (0.35), residues: 582 helix: 2.04 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -1.21 (0.54), residues: 127 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 0.022 0.001 PHE R 221 TYR 0.019 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 86 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8032 (mt) cc_final: 0.7817 (mt) REVERT: R 216 GLN cc_start: 0.7736 (mt0) cc_final: 0.7465 (mt0) REVERT: R 246 ASP cc_start: 0.6649 (m-30) cc_final: 0.6204 (m-30) REVERT: R 276 PHE cc_start: 0.6399 (t80) cc_final: 0.6018 (m-10) REVERT: R 280 ILE cc_start: 0.7927 (mt) cc_final: 0.7707 (mp) REVERT: R 413 MET cc_start: 0.6767 (ttm) cc_final: 0.6412 (ttm) REVERT: R 511 ASP cc_start: 0.7589 (t0) cc_final: 0.7371 (t0) REVERT: R 678 TRP cc_start: 0.6635 (t60) cc_final: 0.5995 (t60) outliers start: 15 outliers final: 5 residues processed: 79 average time/residue: 0.9294 time to fit residues: 77.4205 Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.0770 chunk 55 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.155291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123940 restraints weight = 5457.167| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.94 r_work: 0.3366 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2631 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= 0.184 Angle : 0.538 9.712 6696 Z= 0.269 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 11.775 138.719 997 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.55 % Allowed : 13.92 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.16 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 193 HIS 0.002 0.001 HIS R 310 PHE 0.020 0.001 PHE R 221 TYR 0.016 0.001 TYR R 451 ARG 0.004 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 86 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8079 (mt) cc_final: 0.7837 (mt) REVERT: R 235 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6386 (mtm-85) REVERT: R 236 LYS cc_start: 0.7170 (mppt) cc_final: 0.6895 (mppt) REVERT: R 276 PHE cc_start: 0.6434 (t80) cc_final: 0.6044 (m-10) REVERT: R 280 ILE cc_start: 0.7909 (mt) cc_final: 0.7694 (mp) REVERT: R 299 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7183 (mm-30) REVERT: R 413 MET cc_start: 0.6701 (ttm) cc_final: 0.6360 (ttm) REVERT: R 678 TRP cc_start: 0.6602 (t60) cc_final: 0.6019 (t60) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.9085 time to fit residues: 80.3723 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.154910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123740 restraints weight = 5361.678| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.91 r_work: 0.3346 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2705 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= 0.196 Angle : 0.561 10.308 6696 Z= 0.275 Chirality : 0.041 0.144 809 Planarity : 0.004 0.047 776 Dihedral : 11.326 130.374 997 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.55 % Allowed : 15.49 % Favored : 81.96 % 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: 2.27 (0.35), residues: 582 helix: 2.17 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.21 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 193 HIS 0.002 0.001 HIS R 310 PHE 0.022 0.001 PHE R 221 TYR 0.013 0.001 TYR R 451 ARG 0.003 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 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8219 (mt) cc_final: 0.7978 (mt) REVERT: R 235 ARG cc_start: 0.7178 (mtm-85) cc_final: 0.6510 (mtm-85) REVERT: R 236 LYS cc_start: 0.7235 (mppt) cc_final: 0.6984 (mppt) REVERT: R 276 PHE cc_start: 0.6535 (t80) cc_final: 0.6095 (m-10) REVERT: R 280 ILE cc_start: 0.7976 (mt) cc_final: 0.7770 (mp) REVERT: R 299 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7236 (mm-30) REVERT: R 413 MET cc_start: 0.6779 (ttm) cc_final: 0.6423 (ttm) REVERT: R 678 TRP cc_start: 0.6700 (t60) cc_final: 0.6120 (t60) outliers start: 13 outliers final: 6 residues processed: 76 average time/residue: 1.0171 time to fit residues: 81.0666 Evaluate side-chains 69 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 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 216 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 = 0.3797 r_free = 0.3797 target = 0.154444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123293 restraints weight = 5308.249| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.89 r_work: 0.3398 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4915 Z= 0.225 Angle : 0.583 11.006 6696 Z= 0.283 Chirality : 0.041 0.145 809 Planarity : 0.004 0.048 776 Dihedral : 11.175 126.126 997 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.16 % Allowed : 15.69 % 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: 2.20 (0.35), residues: 582 helix: 2.13 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.25 (0.54), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 363 HIS 0.002 0.001 HIS R 310 PHE 0.022 0.001 PHE R 221 TYR 0.014 0.001 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 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8135 (mt) cc_final: 0.7926 (mt) REVERT: R 234 ASP cc_start: 0.6127 (t70) cc_final: 0.5862 (t70) REVERT: R 235 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6474 (mtm-85) REVERT: R 236 LYS cc_start: 0.7237 (mppt) cc_final: 0.7022 (mppt) REVERT: R 246 ASP cc_start: 0.6639 (m-30) cc_final: 0.6243 (m-30) REVERT: R 276 PHE cc_start: 0.6528 (t80) cc_final: 0.6057 (m-10) REVERT: R 280 ILE cc_start: 0.7893 (mt) cc_final: 0.7693 (mp) REVERT: R 413 MET cc_start: 0.6757 (ttm) cc_final: 0.6385 (ttm) REVERT: R 511 ASP cc_start: 0.7600 (t0) cc_final: 0.7385 (t0) REVERT: R 678 TRP cc_start: 0.6674 (t60) cc_final: 0.6074 (t60) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 1.1292 time to fit residues: 94.1640 Evaluate side-chains 69 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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: 0.6980 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.0970 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.155745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124712 restraints weight = 5385.357| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.91 r_work: 0.3356 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4915 Z= 0.186 Angle : 0.565 11.546 6696 Z= 0.276 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.923 121.095 997 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.57 % Allowed : 16.27 % 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: 2.32 (0.35), residues: 582 helix: 2.21 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.21 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 363 HIS 0.002 0.000 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 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 83 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.029 Fit side-chains REVERT: R 41 ARG cc_start: 0.7636 (mtm180) cc_final: 0.6873 (mtm180) REVERT: R 120 LEU cc_start: 0.8163 (mt) cc_final: 0.7938 (mt) REVERT: R 235 ARG cc_start: 0.7219 (mtm-85) cc_final: 0.6608 (mtm-85) REVERT: R 236 LYS cc_start: 0.7220 (mppt) cc_final: 0.7007 (mtmm) REVERT: R 276 PHE cc_start: 0.6591 (t80) cc_final: 0.6104 (m-10) REVERT: R 280 ILE cc_start: 0.7968 (mt) cc_final: 0.7757 (mp) REVERT: R 385 ASP cc_start: 0.8238 (p0) cc_final: 0.7923 (m-30) REVERT: R 413 MET cc_start: 0.6791 (ttm) cc_final: 0.6430 (ttm) REVERT: R 511 ASP cc_start: 0.7667 (t0) cc_final: 0.7465 (t0) REVERT: R 678 TRP cc_start: 0.6697 (t60) cc_final: 0.6103 (t60) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 1.2947 time to fit residues: 113.0923 Evaluate side-chains 74 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 0.0370 chunk 22 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.156094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124885 restraints weight = 5351.637| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.91 r_work: 0.3425 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4915 Z= 0.182 Angle : 0.571 12.084 6696 Z= 0.280 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.502 119.110 994 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 2.38 (0.35), residues: 582 helix: 2.27 (0.24), residues: 460 sheet: None (None), residues: 0 loop : -1.25 (0.54), residues: 122 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 529 TYR 0.013 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 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.520 Fit side-chains REVERT: R 41 ARG cc_start: 0.7545 (mtm180) cc_final: 0.6815 (mtm180) REVERT: R 120 LEU cc_start: 0.8175 (mt) cc_final: 0.7946 (mt) REVERT: R 234 ASP cc_start: 0.6086 (t70) cc_final: 0.5707 (t70) REVERT: R 235 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6416 (mtm-85) REVERT: R 236 LYS cc_start: 0.7192 (mppt) cc_final: 0.6866 (mppt) REVERT: R 276 PHE cc_start: 0.6551 (t80) cc_final: 0.6065 (m-10) REVERT: R 280 ILE cc_start: 0.7929 (mt) cc_final: 0.7721 (mp) REVERT: R 413 MET cc_start: 0.6714 (ttm) cc_final: 0.6349 (ttm) REVERT: R 511 ASP cc_start: 0.7624 (t0) cc_final: 0.7399 (t0) REVERT: R 678 TRP cc_start: 0.6644 (t60) cc_final: 0.6042 (t60) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.9103 time to fit residues: 79.0826 Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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: 0.9980 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123527 restraints weight = 5333.677| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.90 r_work: 0.3407 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4915 Z= 0.219 Angle : 0.584 12.128 6696 Z= 0.290 Chirality : 0.042 0.147 809 Planarity : 0.005 0.048 776 Dihedral : 10.466 118.863 994 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.18 % Allowed : 17.06 % 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: 2.32 (0.35), residues: 582 helix: 2.20 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.20 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 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 70 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.534 Fit side-chains REVERT: R 41 ARG cc_start: 0.7530 (mtm180) cc_final: 0.6897 (mtm180) REVERT: R 120 LEU cc_start: 0.8127 (mt) cc_final: 0.7890 (mt) REVERT: R 235 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6490 (mtm-85) REVERT: R 276 PHE cc_start: 0.6526 (t80) cc_final: 0.6032 (m-10) REVERT: R 280 ILE cc_start: 0.7887 (mt) cc_final: 0.7683 (mp) REVERT: R 413 MET cc_start: 0.6657 (ttm) cc_final: 0.6279 (ttm) REVERT: R 678 TRP cc_start: 0.6662 (t60) cc_final: 0.6075 (t60) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.8965 time to fit residues: 65.3885 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 : 0.488 ------------------------------------------------------------------------------- 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: 0.3980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 10 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.155820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124384 restraints weight = 5407.126| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.92 r_work: 0.3345 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4915 Z= 0.182 Angle : 0.576 11.859 6696 Z= 0.284 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.276 117.907 994 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.18 % Allowed : 17.45 % Favored : 81.37 % 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: 2.46 (0.35), residues: 582 helix: 2.29 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.12 (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 0.030 0.001 PHE R 529 TYR 0.014 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: 3773.70 seconds wall clock time: 66 minutes 53.44 seconds (4013.44 seconds total)