Starting phenix.real_space_refine on Thu Jul 2 00:40:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y56_38930/07_2026/8y56_38930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y56_38930/07_2026/8y56_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y56_38930/07_2026/8y56_38930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y56_38930/07_2026/8y56_38930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y56_38930/07_2026/8y56_38930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y56_38930/07_2026/8y56_38930.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 194 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CLR': 5, 'DKB': 1} Classifications: {'undetermined': 6, 'water': 5} Link IDs: {None: 10} Chain breaks: 1 Time building chain proxies: 1.15, per 1000 atoms: 0.24 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: 0.49 Conformation dependent library (CDL) restraints added in 204.9 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: 0.13 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: 0.74 Time building geometry restraints manager: 0.60 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: 1.070 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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= 0.365 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 : 13.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (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 ARG 0.002 0.000 ARG R 295 TYR 0.010 0.001 TYR R 451 PHE 0.046 0.001 PHE R 708 TRP 0.008 0.001 TRP R 100 HIS 0.002 0.001 HIS R 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.37 ( 4915) covalent geometry : angle 0.72728 / 0.40 ( 6696) hydrogen bonds : bond 0.24913 / 16.74 ( 355) hydrogen bonds : angle 7.25724 / 5.23 ( 1056) *********************** 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 : 0.169 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: 0.4325 time to fit residues: 42.6310 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 : 0.108 ------------------------------------------------------------------------------- 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 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3783 r_free = 0.3783 target = 0.153456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122256 restraints weight = 5393.958| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.92 r_work: 0.3313 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4915 Z= 0.173 Angle : 0.644 8.076 6696 Z= 0.320 Chirality : 0.044 0.150 809 Planarity : 0.005 0.046 776 Dihedral : 14.095 173.540 997 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.30 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.35), residues: 582 helix: 1.74 (0.24), residues: 465 sheet: None (None), residues: 0 loop : -1.11 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 687 TYR 0.022 0.002 TYR R 451 PHE 0.031 0.002 PHE R 231 TRP 0.005 0.001 TRP R 396 HIS 0.003 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 4915) covalent geometry : angle 0.64396 / 0.32 ( 6696) hydrogen bonds : bond 0.05327 / 3.59 ( 355) hydrogen bonds : angle 4.42398 / 3.18 ( 1056) *********************** 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 : 0.118 Fit side-chains REVERT: R 103 LEU cc_start: 0.8049 (tp) cc_final: 0.7575 (mm) REVERT: R 120 LEU cc_start: 0.7959 (mt) cc_final: 0.7750 (mt) REVERT: R 143 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: R 276 PHE cc_start: 0.6354 (t80) cc_final: 0.6093 (m-10) REVERT: R 301 LEU cc_start: 0.7671 (mm) cc_final: 0.7365 (mm) REVERT: R 413 MET cc_start: 0.6749 (ttm) cc_final: 0.6419 (ttm) REVERT: R 678 TRP cc_start: 0.6715 (t60) cc_final: 0.5983 (t60) outliers start: 11 outliers final: 3 residues processed: 79 average time/residue: 0.4364 time to fit residues: 36.1350 Evaluate side-chains 75 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 GLN R 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122989 restraints weight = 5325.118| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.89 r_work: 0.3319 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2195 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= 0.145 Angle : 0.558 8.653 6696 Z= 0.280 Chirality : 0.041 0.143 809 Planarity : 0.005 0.047 776 Dihedral : 12.975 162.559 997 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.14 % Allowed : 11.18 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.35), residues: 582 helix: 1.96 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -0.94 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 235 TYR 0.019 0.001 TYR R 451 PHE 0.023 0.001 PHE R 221 TRP 0.004 0.001 TRP R 193 HIS 0.002 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4915) covalent geometry : angle 0.55805 / 0.28 ( 6696) hydrogen bonds : bond 0.04732 / 3.16 ( 355) hydrogen bonds : angle 4.12427 / 2.98 ( 1056) *********************** 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 94 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: R 120 LEU cc_start: 0.8066 (mt) cc_final: 0.7835 (mt) REVERT: R 143 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: R 236 LYS cc_start: 0.7187 (mppt) cc_final: 0.6866 (mppt) REVERT: R 246 ASP cc_start: 0.6867 (m-30) cc_final: 0.6424 (m-30) REVERT: R 276 PHE cc_start: 0.6447 (t80) cc_final: 0.6064 (m-10) REVERT: R 280 ILE cc_start: 0.8011 (mt) cc_final: 0.7789 (mp) REVERT: R 301 LEU cc_start: 0.7785 (mm) cc_final: 0.7496 (mm) REVERT: R 302 ASP cc_start: 0.7530 (t70) cc_final: 0.7096 (t70) REVERT: R 303 LYS cc_start: 0.6839 (pptt) cc_final: 0.6605 (mmmt) REVERT: R 381 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7323 (t0) REVERT: R 511 ASP cc_start: 0.7619 (t0) cc_final: 0.7405 (t0) REVERT: R 678 TRP cc_start: 0.6727 (t60) cc_final: 0.6089 (t60) outliers start: 16 outliers final: 5 residues processed: 86 average time/residue: 0.4043 time to fit residues: 36.6969 Evaluate side-chains 75 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 381 ASN 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 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3814 r_free = 0.3814 target = 0.156431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125838 restraints weight = 5327.606| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.89 r_work: 0.3343 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2439 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= 0.122 Angle : 0.527 9.325 6696 Z= 0.265 Chirality : 0.040 0.146 809 Planarity : 0.004 0.047 776 Dihedral : 12.296 152.698 997 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.75 % Allowed : 13.92 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.35), residues: 582 helix: 2.16 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.02 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 235 TYR 0.016 0.001 TYR R 451 PHE 0.020 0.001 PHE R 221 TRP 0.004 0.001 TRP R 193 HIS 0.002 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 4915) covalent geometry : angle 0.52732 / 0.26 ( 6696) hydrogen bonds : bond 0.04163 / 2.77 ( 355) hydrogen bonds : angle 3.93901 / 2.85 ( 1056) *********************** 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 91 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.173 Fit side-chains REVERT: R 120 LEU cc_start: 0.8073 (mt) cc_final: 0.7828 (mt) REVERT: R 236 LYS cc_start: 0.7189 (mppt) cc_final: 0.6955 (mppt) REVERT: R 276 PHE cc_start: 0.6383 (t80) cc_final: 0.6031 (m-10) REVERT: R 280 ILE cc_start: 0.7941 (mt) cc_final: 0.7722 (mp) REVERT: R 385 ASP cc_start: 0.8224 (p0) cc_final: 0.7903 (m-30) REVERT: R 413 MET cc_start: 0.6735 (ttm) cc_final: 0.6413 (ttm) REVERT: R 678 TRP cc_start: 0.6597 (t60) cc_final: 0.5991 (t60) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 0.4443 time to fit residues: 39.1634 Evaluate side-chains 71 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3780 r_free = 0.3780 target = 0.153009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123066 restraints weight = 5387.437| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.85 r_work: 0.3393 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4915 Z= 0.157 Angle : 0.582 9.802 6696 Z= 0.286 Chirality : 0.042 0.144 809 Planarity : 0.004 0.047 776 Dihedral : 11.699 143.550 994 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.33 % Allowed : 14.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.35), residues: 582 helix: 2.05 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.19 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 235 TYR 0.014 0.001 TYR R 451 PHE 0.023 0.002 PHE R 221 TRP 0.005 0.001 TRP R 193 HIS 0.002 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 4915) covalent geometry : angle 0.58175 / 0.29 ( 6696) hydrogen bonds : bond 0.04414 / 2.96 ( 355) hydrogen bonds : angle 3.97623 / 2.88 ( 1056) *********************** 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 85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.178 Fit side-chains REVERT: R 120 LEU cc_start: 0.8119 (mt) cc_final: 0.7883 (mt) REVERT: R 215 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7561 (mm) REVERT: R 235 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.6589 (mtm-85) REVERT: R 236 LYS cc_start: 0.7223 (mppt) cc_final: 0.6948 (mtmm) REVERT: R 276 PHE cc_start: 0.6504 (t80) cc_final: 0.6119 (m-10) REVERT: R 303 LYS cc_start: 0.6571 (mmmt) cc_final: 0.5975 (pptt) REVERT: R 381 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.6995 (t0) REVERT: R 413 MET cc_start: 0.6797 (ttm) cc_final: 0.6446 (ttm) REVERT: R 678 TRP cc_start: 0.6692 (t60) cc_final: 0.6113 (t60) outliers start: 17 outliers final: 6 residues processed: 81 average time/residue: 0.4489 time to fit residues: 38.2046 Evaluate side-chains 71 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 381 ASN 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 54 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.0170 chunk 23 optimal weight: 0.0020 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3800 r_free = 0.3800 target = 0.155012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124818 restraints weight = 5415.285| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.87 r_work: 0.3411 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2667 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= 0.127 Angle : 0.569 10.562 6696 Z= 0.276 Chirality : 0.041 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 11.151 132.167 994 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.75 % Allowed : 15.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.35), residues: 582 helix: 2.19 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.24 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 235 TYR 0.013 0.001 TYR R 451 PHE 0.021 0.001 PHE R 221 TRP 0.004 0.001 TRP R 363 HIS 0.001 0.000 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 4915) covalent geometry : angle 0.56893 / 0.28 ( 6696) hydrogen bonds : bond 0.04092 / 2.73 ( 355) hydrogen bonds : angle 3.90382 / 2.84 ( 1056) *********************** 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 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.179 Fit side-chains REVERT: R 41 ARG cc_start: 0.7567 (mtm180) cc_final: 0.6809 (mtm180) REVERT: R 120 LEU cc_start: 0.8106 (mt) cc_final: 0.7863 (mt) REVERT: R 215 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7517 (mm) REVERT: R 235 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6488 (mtm-85) REVERT: R 236 LYS cc_start: 0.7213 (mppt) cc_final: 0.6971 (mppt) REVERT: R 276 PHE cc_start: 0.6422 (t80) cc_final: 0.5930 (m-10) REVERT: R 299 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7097 (mm-30) REVERT: R 385 ASP cc_start: 0.8143 (p0) cc_final: 0.7831 (m-30) REVERT: R 413 MET cc_start: 0.6699 (ttm) cc_final: 0.6347 (ttm) REVERT: R 678 TRP cc_start: 0.6621 (t60) cc_final: 0.6008 (t60) outliers start: 14 outliers final: 6 residues processed: 80 average time/residue: 0.4460 time to fit residues: 37.4217 Evaluate side-chains 71 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 215 LEU 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 39 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.153108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121948 restraints weight = 5420.010| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.91 r_work: 0.3314 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2711 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= 0.154 Angle : 0.591 11.440 6696 Z= 0.288 Chirality : 0.042 0.145 809 Planarity : 0.004 0.048 776 Dihedral : 10.900 128.031 994 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.75 % Allowed : 15.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.35), residues: 582 helix: 2.10 (0.24), residues: 460 sheet: None (None), residues: 0 loop : -1.33 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 235 TYR 0.014 0.001 TYR R 451 PHE 0.023 0.002 PHE R 221 TRP 0.005 0.001 TRP R 363 HIS 0.002 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 4915) covalent geometry : angle 0.59137 / 0.29 ( 6696) hydrogen bonds : bond 0.04355 / 2.92 ( 355) hydrogen bonds : angle 3.99529 / 2.92 ( 1056) *********************** 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 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.175 Fit side-chains REVERT: R 120 LEU cc_start: 0.8155 (mt) cc_final: 0.7936 (mt) REVERT: R 215 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7548 (mm) REVERT: R 235 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6558 (mtm-85) REVERT: R 236 LYS cc_start: 0.7245 (mppt) cc_final: 0.6988 (mppt) REVERT: R 246 ASP cc_start: 0.6724 (m-30) cc_final: 0.6296 (m-30) REVERT: R 276 PHE cc_start: 0.6231 (t80) cc_final: 0.5804 (m-10) REVERT: R 381 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7013 (t0) REVERT: R 413 MET cc_start: 0.6779 (ttm) cc_final: 0.6411 (ttm) REVERT: R 511 ASP cc_start: 0.7617 (t0) cc_final: 0.7404 (t0) REVERT: R 678 TRP cc_start: 0.6709 (t60) cc_final: 0.6106 (t60) outliers start: 14 outliers final: 6 residues processed: 82 average time/residue: 0.3956 time to fit residues: 34.2010 Evaluate side-chains 75 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 381 ASN 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 41 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.153336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122253 restraints weight = 5457.315| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.91 r_work: 0.3321 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4915 Z= 0.160 Angle : 0.606 12.016 6696 Z= 0.296 Chirality : 0.042 0.145 809 Planarity : 0.004 0.048 776 Dihedral : 10.801 125.087 994 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.16 % Allowed : 15.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.35), residues: 582 helix: 2.07 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.30 (0.54), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 235 TYR 0.015 0.001 TYR R 451 PHE 0.024 0.002 PHE R 221 TRP 0.004 0.001 TRP R 363 HIS 0.002 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 4915) covalent geometry : angle 0.60563 / 0.30 ( 6696) hydrogen bonds : bond 0.04405 / 2.94 ( 355) hydrogen bonds : angle 4.01921 / 2.94 ( 1056) *********************** 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 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.183 Fit side-chains REVERT: R 93 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7367 (tt) REVERT: R 120 LEU cc_start: 0.8039 (mt) cc_final: 0.7820 (mt) REVERT: R 215 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7486 (mm) REVERT: R 235 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6465 (mtm-85) REVERT: R 236 LYS cc_start: 0.7217 (mppt) cc_final: 0.6971 (mptp) REVERT: R 276 PHE cc_start: 0.6219 (t80) cc_final: 0.5769 (m-10) REVERT: R 381 ASN cc_start: 0.7474 (OUTLIER) cc_final: 0.7187 (t0) REVERT: R 413 MET cc_start: 0.6645 (ttm) cc_final: 0.6262 (ttm) REVERT: R 511 ASP cc_start: 0.7573 (t0) cc_final: 0.7372 (t0) REVERT: R 678 TRP cc_start: 0.6634 (t60) cc_final: 0.6042 (t60) outliers start: 11 outliers final: 6 residues processed: 80 average time/residue: 0.4182 time to fit residues: 35.2551 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 SER 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 215 LEU Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 381 ASN 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 34 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3802 r_free = 0.3802 target = 0.154809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123679 restraints weight = 5374.591| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.91 r_work: 0.3401 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4915 Z= 0.140 Angle : 0.595 11.922 6696 Z= 0.289 Chirality : 0.042 0.145 809 Planarity : 0.004 0.047 776 Dihedral : 10.613 120.703 994 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.96 % Allowed : 16.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.35), residues: 582 helix: 2.12 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.22 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 235 TYR 0.014 0.001 TYR R 451 PHE 0.022 0.001 PHE R 221 TRP 0.004 0.001 TRP R 679 HIS 0.002 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4915) covalent geometry : angle 0.59527 / 0.29 ( 6696) hydrogen bonds : bond 0.04205 / 2.80 ( 355) hydrogen bonds : angle 3.96274 / 2.90 ( 1056) *********************** 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 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.176 Fit side-chains REVERT: R 120 LEU cc_start: 0.8147 (mt) cc_final: 0.7913 (mt) REVERT: R 215 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7473 (mm) REVERT: R 227 ILE cc_start: 0.7670 (mm) cc_final: 0.7381 (mp) REVERT: R 235 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6435 (mtm-85) REVERT: R 236 LYS cc_start: 0.7239 (mppt) cc_final: 0.6978 (mptp) REVERT: R 276 PHE cc_start: 0.6410 (t80) cc_final: 0.5948 (m-10) REVERT: R 381 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7022 (t0) REVERT: R 413 MET cc_start: 0.6645 (ttm) cc_final: 0.6266 (ttm) REVERT: R 511 ASP cc_start: 0.7664 (t0) cc_final: 0.7444 (t0) REVERT: R 678 TRP cc_start: 0.6651 (t60) cc_final: 0.6047 (t60) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.3948 time to fit residues: 31.7484 Evaluate side-chains 73 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 381 ASN 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 26 optimal weight: 0.2980 chunk 47 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3823 r_free = 0.3823 target = 0.156869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125848 restraints weight = 5346.980| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.90 r_work: 0.3359 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2922 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= 0.126 Angle : 0.571 12.104 6696 Z= 0.282 Chirality : 0.041 0.146 809 Planarity : 0.004 0.047 776 Dihedral : 10.408 117.592 994 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.37 % Allowed : 16.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.35), residues: 582 helix: 2.23 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -1.17 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 235 TYR 0.013 0.001 TYR R 451 PHE 0.021 0.001 PHE R 221 TRP 0.004 0.001 TRP R 363 HIS 0.001 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 4915) covalent geometry : angle 0.57066 / 0.28 ( 6696) hydrogen bonds : bond 0.03979 / 2.65 ( 355) hydrogen bonds : angle 3.89007 / 2.85 ( 1056) ********************** 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 84 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.183 Fit side-chains REVERT: R 120 LEU cc_start: 0.8128 (mt) cc_final: 0.7895 (mt) REVERT: R 227 ILE cc_start: 0.7623 (mm) cc_final: 0.7325 (mp) REVERT: R 235 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6373 (mtm-85) REVERT: R 236 LYS cc_start: 0.7231 (mppt) cc_final: 0.6990 (mptp) REVERT: R 276 PHE cc_start: 0.6386 (t80) cc_final: 0.5861 (m-10) REVERT: R 381 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7110 (t0) REVERT: R 385 ASP cc_start: 0.8177 (p0) cc_final: 0.7815 (m-30) REVERT: R 511 ASP cc_start: 0.7640 (t0) cc_final: 0.7432 (t0) REVERT: R 678 TRP cc_start: 0.6650 (t60) cc_final: 0.5994 (t60) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.3811 time to fit residues: 33.5714 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 381 ASN 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 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3790 r_free = 0.3790 target = 0.153607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122446 restraints weight = 5380.804| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.90 r_work: 0.3346 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4915 Z= 0.169 Angle : 0.617 10.214 6696 Z= 0.307 Chirality : 0.043 0.171 809 Planarity : 0.005 0.048 776 Dihedral : 10.460 118.307 994 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.96 % Allowed : 16.47 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.35), residues: 582 helix: 2.09 (0.24), residues: 462 sheet: None (None), residues: 0 loop : -1.24 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 235 TYR 0.015 0.002 TYR R 451 PHE 0.024 0.002 PHE R 529 TRP 0.004 0.001 TRP R 363 HIS 0.002 0.001 HIS R 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 4915) covalent geometry : angle 0.61654 / 0.31 ( 6696) hydrogen bonds : bond 0.04377 / 2.94 ( 355) hydrogen bonds : angle 4.02277 / 2.95 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.76 seconds wall clock time: 30 minutes 9.81 seconds (1809.81 seconds total)