Starting phenix.real_space_refine on Sat Aug 23 23:40:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ces_45517/08_2025/9ces_45517_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ces_45517/08_2025/9ces_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2025/9ces_45517_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2025/9ces_45517_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2025/9ces_45517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2025/9ces_45517.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 2.59, 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: 1.26 Conformation dependent library (CDL) restraints added in 344.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.68 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: 2.98 Time building geometry restraints manager: 1.71 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: 25375 2.71 - 5.41: 3355 5.41 - 8.12: 707 8.12 - 10.82: 37 10.82 - 13.53: 19 Bond angle restraints: 29493 Sorted by residual: 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 angle pdb=" C4' G W 79 " pdb=" O4' G W 79 " pdb=" C1' G W 79 " ideal model delta sigma weight residual 109.70 100.22 9.48 1.00e+00 1.00e+00 8.99e+01 angle pdb=" O4' C W 81 " pdb=" C1' C W 81 " pdb=" C2' C W 81 " ideal model delta sigma weight residual 105.80 96.55 9.25 1.00e+00 1.00e+00 8.55e+01 angle pdb=" O3' A W 82 " pdb=" C3' A W 82 " pdb=" C2' A W 82 " ideal model delta sigma weight residual 109.50 123.03 -13.53 1.50e+00 4.44e-01 8.13e+01 angle pdb=" C4' U W 41 " pdb=" C3' U W 41 " pdb=" C2' U W 41 " ideal model delta sigma weight residual 102.60 94.59 8.01 1.00e+00 1.00e+00 6.41e+01 ... (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: 1216 0.105 - 0.210: 328 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: 2.790 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: 0.020 Set scattering table: 0.030 Process input model: 16.060 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4396 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 : 0.013 0.057 9403 Z= 0.791 Angle : 1.955 13.527 13534 Z= 1.297 Chirality : 0.096 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 aren 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 covalent geometry : bond 0.01345 ( 9403) covalent geometry : angle 1.95536 (13534) hydrogen bonds : bond 0.14811 ( 396) hydrogen bonds : angle 7.94823 ( 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 : 0.255 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: 0.3053 time to fit residues: 48.9370 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 : 0.267 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 0.9980 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: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.232369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.188442 restraints weight = 33305.878| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.59 r_work: 0.3976 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9403 Z= 0.203 Angle : 0.831 10.785 13534 Z= 0.457 Chirality : 0.047 0.291 1597 Planarity : 0.005 0.042 1055 Dihedral : 25.131 166.454 3246 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 8.91 % Favored : 89.45 % 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 aren not related in a simple way. whole: 0.61 (0.34), residues: 604 helix: 1.18 (0.29), residues: 318 sheet: -1.79 (0.59), residues: 53 loop : 0.03 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 42 TYR 0.011 0.001 TYR P 45 PHE 0.017 0.002 PHE P 67 TRP 0.014 0.001 TRP P 655 HIS 0.005 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9403) covalent geometry : angle 0.83066 (13534) hydrogen bonds : bond 0.06839 ( 396) hydrogen bonds : angle 4.59644 ( 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 90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 140 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7930 (pttt) REVERT: P 484 GLN cc_start: 0.5177 (tp-100) cc_final: 0.4831 (pt0) REVERT: P 492 MET cc_start: 0.7129 (mmm) cc_final: 0.6896 (tpt) outliers start: 9 outliers final: 4 residues processed: 88 average time/residue: 0.1877 time to fit residues: 22.1867 Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 654 TRP Chi-restraints excluded: chain P residue 667 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.228334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.182422 restraints weight = 33472.127| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 3.41 r_work: 0.3864 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9403 Z= 0.207 Angle : 0.727 6.860 13534 Z= 0.404 Chirality : 0.042 0.214 1597 Planarity : 0.006 0.058 1055 Dihedral : 24.939 174.644 3245 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.00 % Allowed : 10.36 % 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 aren not related in a simple way. whole: 0.49 (0.34), residues: 604 helix: 1.13 (0.29), residues: 317 sheet: -1.75 (0.67), residues: 51 loop : -0.15 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 42 TYR 0.018 0.002 TYR P 475 PHE 0.017 0.002 PHE P 260 TRP 0.007 0.001 TRP P 364 HIS 0.005 0.001 HIS P 146 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9403) covalent geometry : angle 0.72655 (13534) hydrogen bonds : bond 0.06781 ( 396) hydrogen bonds : angle 4.48512 ( 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 78 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6521 (mtt90) REVERT: P 140 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7971 (pttt) REVERT: P 484 GLN cc_start: 0.6170 (tp-100) cc_final: 0.5821 (pm20) REVERT: P 614 GLU cc_start: 0.5857 (tm-30) cc_final: 0.5185 (tt0) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.2728 time to fit residues: 25.2756 Evaluate side-chains 69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG 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 464 LEU Chi-restraints excluded: chain P residue 499 SER 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: 0.9980 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4796 r_free = 0.4796 target = 0.228664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.173505 restraints weight = 32496.983| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.88 r_work: 0.3975 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9403 Z= 0.175 Angle : 0.638 6.460 13534 Z= 0.351 Chirality : 0.038 0.178 1597 Planarity : 0.005 0.047 1055 Dihedral : 24.822 179.812 3245 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.00 % Allowed : 11.09 % 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 aren not related in a simple way. whole: 0.77 (0.35), residues: 604 helix: 1.45 (0.29), residues: 316 sheet: -1.75 (0.60), residues: 58 loop : -0.06 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 81 TYR 0.011 0.001 TYR P 105 PHE 0.016 0.002 PHE P 67 TRP 0.008 0.001 TRP P 227 HIS 0.008 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9403) covalent geometry : angle 0.63817 (13534) hydrogen bonds : bond 0.06035 ( 396) hydrogen bonds : angle 4.19927 ( 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: 11 poor density : 66 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 492 MET cc_start: 0.7315 (mmm) cc_final: 0.7057 (mmp) REVERT: P 560 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7640 (mtm180) REVERT: P 614 GLU cc_start: 0.5790 (tm-30) cc_final: 0.4849 (tt0) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.2073 time to fit residues: 20.9347 Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 432 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 522 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.231537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.187508 restraints weight = 32808.179| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 2.86 r_work: 0.3950 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9403 Z= 0.142 Angle : 0.590 6.387 13534 Z= 0.325 Chirality : 0.036 0.157 1597 Planarity : 0.004 0.037 1055 Dihedral : 24.609 176.636 3245 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.00 % Allowed : 11.82 % Favored : 86.18 % 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 aren not related in a simple way. whole: 1.14 (0.35), residues: 604 helix: 1.82 (0.30), residues: 317 sheet: -1.60 (0.62), residues: 58 loop : 0.00 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 319 TYR 0.011 0.001 TYR P 44 PHE 0.010 0.001 PHE P 67 TRP 0.006 0.001 TRP P 335 HIS 0.008 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9403) covalent geometry : angle 0.58966 (13534) hydrogen bonds : bond 0.05386 ( 396) hydrogen bonds : angle 3.90080 ( 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 76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7071 (mtt90) REVERT: P 560 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7682 (mtm180) REVERT: P 614 GLU cc_start: 0.5783 (tm-30) cc_final: 0.4972 (tt0) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.2559 time to fit residues: 24.5071 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 : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG 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 432 ASP 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 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: 5.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.224608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178193 restraints weight = 32192.632| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.26 r_work: 0.3784 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9403 Z= 0.329 Angle : 0.772 6.364 13534 Z= 0.419 Chirality : 0.044 0.181 1597 Planarity : 0.007 0.084 1055 Dihedral : 25.011 178.497 3245 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.36 % Allowed : 13.09 % Favored : 84.55 % 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 aren not related in a simple way. whole: 0.05 (0.34), residues: 604 helix: 0.76 (0.28), residues: 316 sheet: -1.57 (0.71), residues: 51 loop : -0.45 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 602 TYR 0.025 0.003 TYR P 445 PHE 0.030 0.003 PHE P 260 TRP 0.010 0.002 TRP P 335 HIS 0.005 0.002 HIS P 641 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 9403) covalent geometry : angle 0.77159 (13534) hydrogen bonds : bond 0.07878 ( 396) hydrogen bonds : angle 4.63170 ( 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 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7675 (mtt90) REVERT: P 133 ASP cc_start: 0.8175 (t0) cc_final: 0.7892 (t0) REVERT: P 503 MET cc_start: 0.7640 (mtp) cc_final: 0.7332 (mtt) REVERT: P 560 ARG cc_start: 0.8314 (mtt90) cc_final: 0.7817 (mtm180) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.2400 time to fit residues: 21.5637 Evaluate side-chains 69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 43 SER 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 432 ASP Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 522 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 48 optimal weight: 0.0970 chunk 64 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.232151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.188983 restraints weight = 33689.480| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 3.12 r_work: 0.3909 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9403 Z= 0.132 Angle : 0.592 6.540 13534 Z= 0.323 Chirality : 0.036 0.163 1597 Planarity : 0.005 0.067 1055 Dihedral : 24.659 179.000 3245 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.00 % Allowed : 13.45 % Favored : 84.55 % 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 aren not related in a simple way. whole: 1.14 (0.35), residues: 604 helix: 1.79 (0.30), residues: 317 sheet: -1.54 (0.68), residues: 53 loop : -0.02 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 270 TYR 0.012 0.001 TYR P 45 PHE 0.012 0.001 PHE P 67 TRP 0.007 0.001 TRP P 577 HIS 0.007 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9403) covalent geometry : angle 0.59179 (13534) hydrogen bonds : bond 0.05358 ( 396) hydrogen bonds : angle 3.90487 ( 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 74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7361 (mpt180) REVERT: P 503 MET cc_start: 0.7440 (mtp) cc_final: 0.7115 (mtt) REVERT: P 560 ARG cc_start: 0.8268 (mtt90) cc_final: 0.7791 (mtm180) REVERT: P 614 GLU cc_start: 0.5925 (tm-30) cc_final: 0.5001 (tt0) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.2405 time to fit residues: 22.3876 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 : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG 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 432 ASP Chi-restraints excluded: chain P residue 489 HIS 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 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: 0.5980 chunk 64 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.231850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.188846 restraints weight = 33960.816| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 3.10 r_work: 0.3924 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9403 Z= 0.146 Angle : 0.583 6.111 13534 Z= 0.320 Chirality : 0.035 0.161 1597 Planarity : 0.005 0.061 1055 Dihedral : 24.574 179.254 3245 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.82 % Allowed : 13.64 % Favored : 84.55 % 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 aren not related in a simple way. whole: 1.21 (0.36), residues: 604 helix: 1.88 (0.30), residues: 317 sheet: -1.47 (0.68), residues: 53 loop : -0.05 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 270 TYR 0.010 0.001 TYR P 105 PHE 0.011 0.001 PHE P 67 TRP 0.017 0.001 TRP P 577 HIS 0.006 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9403) covalent geometry : angle 0.58276 (13534) hydrogen bonds : bond 0.05392 ( 396) hydrogen bonds : angle 3.93058 ( 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 72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6486 (mtt90) REVERT: P 503 MET cc_start: 0.7514 (mtp) cc_final: 0.7203 (mtt) REVERT: P 560 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7812 (mtm180) REVERT: P 614 GLU cc_start: 0.5813 (tm-30) cc_final: 0.4845 (tt0) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.2323 time to fit residues: 21.6162 Evaluate side-chains 69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG 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 432 ASP Chi-restraints excluded: chain P residue 489 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.229921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.185285 restraints weight = 33579.649| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.01 r_work: 0.3913 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9403 Z= 0.180 Angle : 0.615 5.936 13534 Z= 0.336 Chirality : 0.037 0.161 1597 Planarity : 0.005 0.061 1055 Dihedral : 24.635 179.766 3245 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.64 % Allowed : 14.18 % Favored : 84.18 % 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 aren not related in a simple way. whole: 0.98 (0.36), residues: 604 helix: 1.61 (0.29), residues: 317 sheet: -1.49 (0.69), residues: 53 loop : -0.04 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 553 TYR 0.013 0.002 TYR P 105 PHE 0.022 0.002 PHE P 49 TRP 0.010 0.001 TRP P 577 HIS 0.005 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9403) covalent geometry : angle 0.61517 (13534) hydrogen bonds : bond 0.05877 ( 396) hydrogen bonds : angle 4.08499 ( 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 70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7489 (mpt180) REVERT: P 503 MET cc_start: 0.7586 (mtp) cc_final: 0.7265 (mtt) REVERT: P 560 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7791 (mtm180) REVERT: P 614 GLU cc_start: 0.5765 (tm-30) cc_final: 0.4719 (tt0) outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.2163 time to fit residues: 19.9602 Evaluate side-chains 69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG 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 432 ASP Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 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: 0.9980 chunk 65 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.230406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.185718 restraints weight = 32747.062| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.98 r_work: 0.3920 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9403 Z= 0.155 Angle : 0.584 5.984 13534 Z= 0.318 Chirality : 0.035 0.160 1597 Planarity : 0.005 0.058 1055 Dihedral : 24.594 179.257 3245 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.64 % Allowed : 14.18 % Favored : 84.18 % 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 aren not related in a simple way. whole: 1.13 (0.36), residues: 604 helix: 1.77 (0.29), residues: 317 sheet: -1.53 (0.68), residues: 53 loop : -0.01 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 270 TYR 0.011 0.001 TYR P 105 PHE 0.018 0.002 PHE P 49 TRP 0.007 0.001 TRP P 335 HIS 0.005 0.001 HIS P 68 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9403) covalent geometry : angle 0.58412 (13534) hydrogen bonds : bond 0.05440 ( 396) hydrogen bonds : angle 3.94742 ( 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 75 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7444 (mpt180) REVERT: P 503 MET cc_start: 0.7571 (mtp) cc_final: 0.7242 (mtt) REVERT: P 560 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7806 (mtm180) REVERT: P 614 GLU cc_start: 0.5813 (tm-30) cc_final: 0.4850 (tt0) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.2792 time to fit residues: 26.7595 Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 ARG 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 432 ASP Chi-restraints excluded: chain P residue 489 HIS Chi-restraints excluded: chain P residue 499 SER Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 654 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.226405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.181827 restraints weight = 33633.001| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.05 r_work: 0.3852 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.7293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9403 Z= 0.288 Angle : 0.716 6.609 13534 Z= 0.388 Chirality : 0.041 0.169 1597 Planarity : 0.006 0.063 1055 Dihedral : 24.894 179.057 3245 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.18 % Allowed : 13.82 % Favored : 84.00 % 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 aren not related in a simple way. whole: 0.24 (0.34), residues: 604 helix: 1.03 (0.29), residues: 310 sheet: -1.68 (0.70), residues: 51 loop : -0.44 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 602 TYR 0.022 0.002 TYR P 105 PHE 0.024 0.003 PHE P 260 TRP 0.008 0.002 TRP P 577 HIS 0.004 0.002 HIS P 641 Details of bonding type rmsd covalent geometry : bond 0.00623 ( 9403) covalent geometry : angle 0.71592 (13534) hydrogen bonds : bond 0.07318 ( 396) hydrogen bonds : angle 4.47603 ( 1030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4116.59 seconds wall clock time: 70 minutes 35.80 seconds (4235.80 seconds total)