Starting phenix.real_space_refine on Fri Jul 3 18:08:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ces_45517/07_2026/9ces_45517_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ces_45517/07_2026/9ces_45517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ces_45517/07_2026/9ces_45517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ces_45517/07_2026/9ces_45517.map" model { file = "/net/cci-nas-00/data/ceres_data/9ces_45517/07_2026/9ces_45517_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ces_45517/07_2026/9ces_45517_neut.cif" } resolution = 3.28 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= 0.002 sd= 0.036 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 181 5.49 5 S 38 5.16 5 C 4897 2.51 5 N 1619 2.21 5 O 2103 1.98 5 H 7001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 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: 15839 Number of models: 1 Model: "" Number of chains: 4 Chain: "N" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 475 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "P" Number of atoms: 10029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 10029 Classifications: {'peptide': 612} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 591} Chain breaks: 3 Chain: "T" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 761 Classifications: {'DNA': 24} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 23} Chain: "W" Number of atoms: 4574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 4574 Classifications: {'RNA': 142} Modifications used: {'3*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 69, 'rna3p_pyr': 50} Link IDs: {'rna2p': 23, 'rna3p': 118} Time building chain proxies: 2.61, per 1000 atoms: 0.16 Number of scatterers: 15839 At special positions: 0 Unit cell: (81.549, 111.384, 166.413, 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 38 16.00 P 181 15.00 O 2103 8.00 N 1619 7.00 C 4897 6.00 H 7001 1.00 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: 1.13 Conformation dependent library (CDL) restraints added in 215.1 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 57.0% alpha, 8.8% beta 54 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'P' and resid 16 through 53 Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 88 through 110 Processing helix chain 'P' and resid 114 through 119 Processing helix chain 'P' and resid 124 through 162 removed outlier: 3.862A pdb=" N ALA P 129 " --> pdb=" O SER P 125 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR P 130 " --> pdb=" O HIS P 126 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER P 131 " --> pdb=" O VAL P 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS P 146 " --> pdb=" O ASN P 142 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER P 148 " --> pdb=" O GLU P 144 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS P 149 " --> pdb=" O ALA P 145 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR P 150 " --> pdb=" O HIS P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 182 Processing helix chain 'P' and resid 217 through 222 removed outlier: 3.943A pdb=" N ASP P 221 " --> pdb=" O PRO P 217 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU P 222 " --> pdb=" O ARG P 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 217 through 222' Processing helix chain 'P' and resid 225 through 228 Processing helix chain 'P' and resid 229 through 243 Processing helix chain 'P' and resid 273 through 281 Processing helix chain 'P' and resid 282 through 298 removed outlier: 4.355A pdb=" N ASP P 288 " --> pdb=" O ASP P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 318 Processing helix chain 'P' and resid 323 through 339 removed outlier: 3.621A pdb=" N ALA P 327 " --> pdb=" O SER P 323 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 351 removed outlier: 3.671A pdb=" N LEU P 350 " --> pdb=" O GLN P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 385 through 387 No H-bonds generated for 'chain 'P' and resid 385 through 387' Processing helix chain 'P' and resid 416 through 421 Processing helix chain 'P' and resid 447 through 454 Processing helix chain 'P' and resid 455 through 470 Processing helix chain 'P' and resid 472 through 479 Processing helix chain 'P' and resid 480 through 483 Processing helix chain 'P' and resid 489 through 512 removed outlier: 3.729A pdb=" N TYR P 496 " --> pdb=" O MET P 492 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG P 502 " --> pdb=" O CYS P 498 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET P 503 " --> pdb=" O SER P 499 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N HIS P 505 " --> pdb=" O LYS P 501 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET P 506 " --> pdb=" O ARG P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 513 through 543 removed outlier: 4.155A pdb=" N ARG P 517 " --> pdb=" O HIS P 513 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR P 524 " --> pdb=" O LYS P 520 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS P 528 " --> pdb=" O TYR P 524 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER P 529 " --> pdb=" O ASN P 525 " (cutoff:3.500A) Processing helix chain 'P' and resid 556 through 564 Processing helix chain 'P' and resid 569 through 571 No H-bonds generated for 'chain 'P' and resid 569 through 571' Processing helix chain 'P' and resid 600 through 604 Processing helix chain 'P' and resid 657 through 670 Processing sheet with id=AA1, first strand: chain 'P' and resid 4 through 10 removed outlier: 6.995A pdb=" N SER P 376 " --> pdb=" O VAL P 371 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL P 371 " --> pdb=" O SER P 376 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER P 378 " --> pdb=" O ALA P 369 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA P 369 " --> pdb=" O SER P 378 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN P 380 " --> pdb=" O ASP P 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 442 through 446 removed outlier: 6.298A pdb=" N LYS P 422 " --> pdb=" O ILE P 574 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLY P 576 " --> pdb=" O LYS P 422 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU P 424 " --> pdb=" O GLY P 576 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY P 578 " --> pdb=" O LEU P 424 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N CYS P 426 " --> pdb=" O GLY P 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 629 through 631 258 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 6984 1.11 - 1.29: 958 1.29 - 1.47: 4240 1.47 - 1.64: 4163 1.64 - 1.82: 59 Bond restraints: 16404 Sorted by residual: bond pdb=" C2 A W 137 " pdb=" H2 A W 137 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C5 U W 41 " pdb=" H5 U W 41 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C8 A W 141 " pdb=" H8 A W 141 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C5 U W 20 " pdb=" H5 U W 20 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASN P 114 " pdb=" H ASN P 114 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 16399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 25364 2.71 - 5.41: 3360 5.41 - 8.12: 714 8.12 - 10.82: 36 10.82 - 13.53: 19 Bond angle restraints: 29493 Sorted by residual: angle pdb=" N6 A W 77 " pdb=" C6 A W 77 " pdb=" N1 A W 77 " ideal model delta sigma weight residual 118.60 110.68 7.92 6.00e-01 2.78e+00 1.74e+02 angle pdb=" N6 A W 127 " pdb=" C6 A W 127 " pdb=" N1 A W 127 " ideal model delta sigma weight residual 118.60 111.31 7.29 6.00e-01 2.78e+00 1.48e+02 angle pdb=" O4' DC T 0 " pdb=" C1' DC T 0 " pdb=" N1 DC T 0 " ideal model delta sigma weight residual 108.00 116.04 -8.04 7.00e-01 2.04e+00 1.32e+02 angle pdb=" N6 A W 17 " pdb=" C6 A W 17 " pdb=" N1 A W 17 " ideal model delta sigma weight residual 118.60 111.82 6.78 6.00e-01 2.78e+00 1.28e+02 angle pdb=" C4' C W 81 " pdb=" O4' C W 81 " pdb=" C1' C W 81 " ideal model delta sigma weight residual 109.70 99.16 10.54 1.00e+00 1.00e+00 1.11e+02 ... (remaining 29488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 6851 33.55 - 67.10: 711 67.10 - 100.65: 92 100.65 - 134.19: 9 134.19 - 167.74: 3 Dihedral angle restraints: 7666 sinusoidal: 5519 harmonic: 2147 Sorted by residual: dihedral pdb=" O4' A W 53 " pdb=" C2' A W 53 " pdb=" C1' A W 53 " pdb=" C3' A W 53 " ideal model delta sinusoidal sigma weight residual 25.00 -28.09 53.09 1 8.00e+00 1.56e-02 5.99e+01 dihedral pdb=" C5' G W 79 " pdb=" C4' G W 79 " pdb=" C3' G W 79 " pdb=" O3' G W 79 " ideal model delta sinusoidal sigma weight residual 147.00 94.16 52.84 1 8.00e+00 1.56e-02 5.94e+01 dihedral pdb=" C3' G W 45 " pdb=" C4' G W 45 " pdb=" O4' G W 45 " pdb=" C1' G W 45 " ideal model delta sinusoidal sigma weight residual 20.00 -32.55 52.55 1 8.00e+00 1.56e-02 5.88e+01 ... (remaining 7663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1201 0.105 - 0.210: 343 0.210 - 0.315: 37 0.315 - 0.420: 14 0.420 - 0.525: 2 Chirality restraints: 1597 Sorted by residual: chirality pdb=" C4' C W 81 " pdb=" C5' C W 81 " pdb=" O4' C W 81 " pdb=" C3' C W 81 " both_signs ideal model delta sigma weight residual False -2.50 -1.98 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C4' A W 43 " pdb=" C5' A W 43 " pdb=" O4' A W 43 " pdb=" C3' A W 43 " both_signs ideal model delta sigma weight residual False -2.50 -2.06 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C4' U W 41 " pdb=" C5' U W 41 " pdb=" O4' U W 41 " pdb=" C3' U W 41 " both_signs ideal model delta sigma weight residual False -2.50 -2.09 -0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 1594 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G W 110 " -0.461 2.00e-02 2.50e+03 1.75e-01 1.07e+03 pdb=" N9 G W 110 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G W 110 " 0.149 2.00e-02 2.50e+03 pdb=" N7 G W 110 " 0.133 2.00e-02 2.50e+03 pdb=" C5 G W 110 " 0.013 2.00e-02 2.50e+03 pdb=" C6 G W 110 " -0.112 2.00e-02 2.50e+03 pdb=" O6 G W 110 " -0.224 2.00e-02 2.50e+03 pdb=" N1 G W 110 " -0.057 2.00e-02 2.50e+03 pdb=" C2 G W 110 " 0.047 2.00e-02 2.50e+03 pdb=" N2 G W 110 " 0.246 2.00e-02 2.50e+03 pdb=" N3 G W 110 " 0.056 2.00e-02 2.50e+03 pdb=" C4 G W 110 " 0.041 2.00e-02 2.50e+03 pdb=" H8 G W 110 " 0.204 2.00e-02 2.50e+03 pdb=" H1 G W 110 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G W 71 " -0.457 2.00e-02 2.50e+03 1.74e-01 1.06e+03 pdb=" N9 G W 71 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G W 71 " 0.156 2.00e-02 2.50e+03 pdb=" N7 G W 71 " 0.049 2.00e-02 2.50e+03 pdb=" C5 G W 71 " -0.021 2.00e-02 2.50e+03 pdb=" C6 G W 71 " -0.109 2.00e-02 2.50e+03 pdb=" O6 G W 71 " -0.237 2.00e-02 2.50e+03 pdb=" N1 G W 71 " -0.024 2.00e-02 2.50e+03 pdb=" C2 G W 71 " 0.045 2.00e-02 2.50e+03 pdb=" N2 G W 71 " 0.198 2.00e-02 2.50e+03 pdb=" N3 G W 71 " 0.043 2.00e-02 2.50e+03 pdb=" C4 G W 71 " 0.032 2.00e-02 2.50e+03 pdb=" H8 G W 71 " 0.268 2.00e-02 2.50e+03 pdb=" H1 G W 71 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C W 81 " 0.377 2.00e-02 2.50e+03 1.85e-01 9.43e+02 pdb=" N1 C W 81 " 0.058 2.00e-02 2.50e+03 pdb=" C2 C W 81 " -0.054 2.00e-02 2.50e+03 pdb=" O2 C W 81 " -0.357 2.00e-02 2.50e+03 pdb=" N3 C W 81 " 0.043 2.00e-02 2.50e+03 pdb=" C4 C W 81 " 0.104 2.00e-02 2.50e+03 pdb=" N4 C W 81 " 0.206 2.00e-02 2.50e+03 pdb=" C5 C W 81 " -0.052 2.00e-02 2.50e+03 pdb=" C6 C W 81 " -0.039 2.00e-02 2.50e+03 pdb=" H5 C W 81 " -0.164 2.00e-02 2.50e+03 pdb=" H6 C W 81 " -0.122 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 770 2.11 - 2.73: 20927 2.73 - 3.35: 44014 3.35 - 3.98: 58796 3.98 - 4.60: 84987 Nonbonded interactions: 209494 Sorted by model distance: nonbonded pdb="HO2' C W 78 " pdb=" H4' G W 79 " model vdw 1.487 2.270 nonbonded pdb="HO2' G W 42 " pdb=" H4' A W 43 " model vdw 1.507 2.270 nonbonded pdb="HO2' C W 81 " pdb=" OP1 A W 82 " model vdw 1.561 2.450 nonbonded pdb="HO2' A W 123 " pdb=" OP2 A W 124 " model vdw 1.563 2.450 nonbonded pdb="HO2' A W 82 " pdb=" OP2 U W 83 " model vdw 1.565 2.450 ... (remaining 209489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 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: 0.090 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.670 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: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4619 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 : 0.014 0.057 9403 Z= 1.170 Angle : 1.958 13.527 13534 Z= 1.884 Chirality : 0.097 0.525 1597 Planarity : 0.034 0.180 1055 Dihedral : 23.225 167.742 4512 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.91 % Allowed : 2.00 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.87 (0.32), residues: 604 helix: -0.39 (0.27), residues: 316 sheet: -1.56 (0.62), residues: 40 loop : -0.41 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 668 TYR 0.074 0.019 TYR P 445 PHE 0.054 0.012 PHE P 519 TRP 0.116 0.021 TRP P 654 HIS 0.012 0.003 HIS P 641 Details of bonding type rmsd/Z covalent geometry : bond 0.01352 / 1.17 ( 9403) covalent geometry : angle 1.95821 / 1.88 (13534) hydrogen bonds : bond 0.14811 / 15.57 ( 396) hydrogen bonds : angle 7.94823 / 8.27 ( 1030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 256 ASN cc_start: 0.5854 (t0) cc_final: 0.5475 (t0) REVERT: P 272 ASP cc_start: 0.7284 (p0) cc_final: 0.7032 (p0) REVERT: P 492 MET cc_start: 0.6846 (mmm) cc_final: 0.6321 (tpt) outliers start: 5 outliers final: 2 residues processed: 134 average time/residue: 0.2851 time to fit residues: 46.5596 Evaluate side-chains 75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 567 VAL Chi-restraints excluded: chain P residue 654 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.231888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.187776 restraints weight = 33592.335| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.55 r_work: 0.3979 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9403 Z= 0.233 Angle : 0.906 9.975 13534 Z= 0.562 Chirality : 0.061 0.560 1597 Planarity : 0.007 0.050 1055 Dihedral : 25.530 170.728 3246 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.00 % Allowed : 8.91 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.00 (0.34), residues: 604 helix: 0.63 (0.28), residues: 322 sheet: -2.25 (0.57), residues: 49 loop : -0.18 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 495 TYR 0.013 0.002 TYR P 45 PHE 0.020 0.002 PHE P 67 TRP 0.020 0.002 TRP P 655 HIS 0.006 0.002 HIS P 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.23 ( 9403) covalent geometry : angle 0.90620 / 0.56 (13534) hydrogen bonds : bond 0.09038 / 9.11 ( 396) hydrogen bonds : angle 5.09842 / 5.76 ( 1030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7252 (mmt90) REVERT: P 140 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7968 (pttt) REVERT: P 272 ASP cc_start: 0.8295 (p0) cc_final: 0.7963 (p0) REVERT: P 484 GLN cc_start: 0.4978 (tp-100) cc_final: 0.4642 (pt0) REVERT: P 567 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.7162 (t) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 0.1724 time to fit residues: 19.3226 Evaluate side-chains 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 567 VAL Chi-restraints excluded: chain P residue 574 ILE Chi-restraints excluded: chain P residue 654 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 40.0000 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.230452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.177141 restraints weight = 33676.660| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 1.90 r_work: 0.4026 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9403 Z= 0.210 Angle : 0.761 9.701 13534 Z= 0.471 Chirality : 0.051 0.284 1597 Planarity : 0.006 0.043 1055 Dihedral : 25.284 167.129 3246 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.00 % Allowed : 8.73 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.15 (0.34), residues: 604 helix: 0.80 (0.28), residues: 318 sheet: -1.94 (0.63), residues: 51 loop : -0.22 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 602 TYR 0.039 0.002 TYR P 475 PHE 0.020 0.002 PHE P 366 TRP 0.009 0.001 TRP P 655 HIS 0.017 0.002 HIS P 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.21 ( 9403) covalent geometry : angle 0.76058 / 0.47 (13534) hydrogen bonds : bond 0.07989 / 8.14 ( 396) hydrogen bonds : angle 4.68420 / 5.33 ( 1030) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 140 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7957 (pttt) REVERT: P 272 ASP cc_start: 0.8219 (p0) cc_final: 0.7956 (p0) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.2042 time to fit residues: 20.6483 Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 504 GLU Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 40.0000 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 68 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 = 0.4804 r_free = 0.4804 target = 0.229391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.183621 restraints weight = 33265.022| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 3.20 r_work: 0.3877 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9403 Z= 0.195 Angle : 0.688 8.555 13534 Z= 0.428 Chirality : 0.047 0.276 1597 Planarity : 0.006 0.041 1055 Dihedral : 25.115 167.379 3245 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.73 % Allowed : 9.64 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.43 (0.35), residues: 604 helix: 1.10 (0.29), residues: 318 sheet: -1.79 (0.66), residues: 51 loop : -0.20 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 85 TYR 0.013 0.002 TYR P 475 PHE 0.021 0.002 PHE P 67 TRP 0.010 0.001 TRP P 655 HIS 0.003 0.001 HIS P 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 9403) covalent geometry : angle 0.68797 / 0.43 (13534) hydrogen bonds : bond 0.07311 / 7.52 ( 396) hydrogen bonds : angle 4.52787 / 5.08 ( 1030) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 140 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7968 (pttt) REVERT: P 272 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8158 (p0) REVERT: P 484 GLN cc_start: 0.6037 (tp-100) cc_final: 0.5371 (pt0) REVERT: P 559 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6334 (ttm) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.1995 time to fit residues: 18.8733 Evaluate side-chains 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 272 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 559 MET Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.231015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.189653 restraints weight = 33495.484| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 3.37 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9403 Z= 0.151 Angle : 0.626 8.896 13534 Z= 0.391 Chirality : 0.044 0.264 1597 Planarity : 0.005 0.038 1055 Dihedral : 25.078 166.562 3245 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.27 % Allowed : 11.45 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.63 (0.35), residues: 604 helix: 1.30 (0.29), residues: 318 sheet: -1.82 (0.66), residues: 53 loop : -0.12 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 81 TYR 0.010 0.001 TYR P 45 PHE 0.025 0.002 PHE P 67 TRP 0.006 0.001 TRP P 227 HIS 0.008 0.001 HIS P 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 ( 9403) covalent geometry : angle 0.62567 / 0.39 (13534) hydrogen bonds : bond 0.06761 / 7.04 ( 396) hydrogen bonds : angle 4.34906 / 4.89 ( 1030) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 69 average time/residue: 0.1951 time to fit residues: 17.9184 Evaluate side-chains 67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.229149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.175825 restraints weight = 33198.199| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.13 r_work: 0.3965 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9403 Z= 0.195 Angle : 0.639 8.782 13534 Z= 0.394 Chirality : 0.043 0.209 1597 Planarity : 0.005 0.042 1055 Dihedral : 25.080 179.081 3245 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.64 % Allowed : 11.64 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.50 (0.35), residues: 604 helix: 1.24 (0.29), residues: 317 sheet: -1.96 (0.66), residues: 53 loop : -0.24 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 602 TYR 0.013 0.002 TYR P 105 PHE 0.017 0.002 PHE P 67 TRP 0.008 0.001 TRP P 335 HIS 0.003 0.001 HIS P 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 ( 9403) covalent geometry : angle 0.63893 / 0.39 (13534) hydrogen bonds : bond 0.07088 / 7.31 ( 396) hydrogen bonds : angle 4.40549 / 4.97 ( 1030) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7772 (mmt-90) cc_final: 0.7381 (mpt180) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.1911 time to fit residues: 17.8150 Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.231134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.186149 restraints weight = 33390.204| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 3.11 r_work: 0.3912 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9403 Z= 0.135 Angle : 0.583 8.544 13534 Z= 0.363 Chirality : 0.041 0.197 1597 Planarity : 0.004 0.038 1055 Dihedral : 25.049 176.882 3245 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.91 % Allowed : 12.18 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.83 (0.36), residues: 604 helix: 1.56 (0.30), residues: 316 sheet: -1.82 (0.64), residues: 58 loop : -0.09 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 42 TYR 0.012 0.001 TYR P 176 PHE 0.025 0.001 PHE P 67 TRP 0.008 0.001 TRP P 655 HIS 0.005 0.001 HIS P 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 ( 9403) covalent geometry : angle 0.58252 / 0.36 (13534) hydrogen bonds : bond 0.06310 / 6.60 ( 396) hydrogen bonds : angle 4.20703 / 4.69 ( 1030) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7830 (mmt-90) cc_final: 0.7445 (mpt180) outliers start: 5 outliers final: 5 residues processed: 64 average time/residue: 0.1812 time to fit residues: 15.7939 Evaluate side-chains 63 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 263 SER Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 568 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.228710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.183254 restraints weight = 33477.548| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 3.31 r_work: 0.3848 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9403 Z= 0.188 Angle : 0.615 8.821 13534 Z= 0.376 Chirality : 0.041 0.201 1597 Planarity : 0.005 0.042 1055 Dihedral : 24.973 175.157 3245 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.45 % Allowed : 12.00 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.55 (0.35), residues: 604 helix: 1.38 (0.29), residues: 315 sheet: -1.98 (0.63), residues: 58 loop : -0.29 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 602 TYR 0.015 0.002 TYR P 105 PHE 0.018 0.002 PHE P 260 TRP 0.007 0.001 TRP P 655 HIS 0.004 0.001 HIS P 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 ( 9403) covalent geometry : angle 0.61543 / 0.38 (13534) hydrogen bonds : bond 0.07000 / 7.23 ( 396) hydrogen bonds : angle 4.33019 / 4.86 ( 1030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7657 (mpt180) outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.1809 time to fit residues: 16.6146 Evaluate side-chains 68 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 310 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.230461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.179294 restraints weight = 33363.057| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.01 r_work: 0.3988 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9403 Z= 0.133 Angle : 0.565 8.413 13534 Z= 0.350 Chirality : 0.040 0.188 1597 Planarity : 0.005 0.039 1055 Dihedral : 24.916 176.021 3245 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.09 % Allowed : 12.36 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.84 (0.35), residues: 604 helix: 1.61 (0.30), residues: 315 sheet: -1.97 (0.68), residues: 53 loop : -0.17 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 42 TYR 0.018 0.001 TYR P 44 PHE 0.023 0.001 PHE P 67 TRP 0.008 0.001 TRP P 655 HIS 0.004 0.001 HIS P 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 ( 9403) covalent geometry : angle 0.56532 / 0.35 (13534) hydrogen bonds : bond 0.06276 / 6.57 ( 396) hydrogen bonds : angle 4.17902 / 4.68 ( 1030) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7564 (mpt180) REVERT: P 560 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7561 (mtm180) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.1636 time to fit residues: 14.3745 Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 310 LEU Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.228494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.182292 restraints weight = 33258.952| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.36 r_work: 0.3839 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9403 Z= 0.190 Angle : 0.602 8.705 13534 Z= 0.366 Chirality : 0.041 0.190 1597 Planarity : 0.005 0.044 1055 Dihedral : 24.878 175.798 3245 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.45 % Allowed : 12.18 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.53 (0.35), residues: 604 helix: 1.40 (0.29), residues: 315 sheet: -1.99 (0.64), residues: 58 loop : -0.38 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 602 TYR 0.016 0.002 TYR P 105 PHE 0.021 0.002 PHE P 260 TRP 0.008 0.001 TRP P 655 HIS 0.006 0.001 HIS P 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 ( 9403) covalent geometry : angle 0.60244 / 0.37 (13534) hydrogen bonds : bond 0.06933 / 7.19 ( 396) hydrogen bonds : angle 4.31713 / 4.85 ( 1030) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7999 (mmt-90) cc_final: 0.7758 (mpt180) REVERT: P 560 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7668 (mtm180) outliers start: 8 outliers final: 8 residues processed: 64 average time/residue: 0.2124 time to fit residues: 18.5477 Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 290 LYS Chi-restraints excluded: chain P residue 310 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 655 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.229666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.176772 restraints weight = 33476.786| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.02 r_work: 0.3980 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9403 Z= 0.151 Angle : 0.564 8.494 13534 Z= 0.346 Chirality : 0.039 0.180 1597 Planarity : 0.005 0.043 1055 Dihedral : 24.856 176.551 3245 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.27 % Allowed : 12.36 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.68 (0.35), residues: 604 helix: 1.49 (0.29), residues: 315 sheet: -1.94 (0.65), residues: 58 loop : -0.25 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 600 TYR 0.012 0.002 TYR P 44 PHE 0.020 0.002 PHE P 67 TRP 0.020 0.001 TRP P 577 HIS 0.004 0.001 HIS P 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 ( 9403) covalent geometry : angle 0.56449 / 0.35 (13534) hydrogen bonds : bond 0.06449 / 6.74 ( 396) hydrogen bonds : angle 4.21881 / 4.71 ( 1030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3640.85 seconds wall clock time: 62 minutes 32.28 seconds (3752.28 seconds total)