Starting phenix.real_space_refine on Fri Sep 11 05:45:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x0l_21978/09_2026/6x0l_21978.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x0l_21978/09_2026/6x0l_21978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x0l_21978/09_2026/6x0l_21978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x0l_21978/09_2026/6x0l_21978.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x0l_21978/09_2026/6x0l_21978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x0l_21978/09_2026/6x0l_21978.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 45 5.16 5 C 4989 2.51 5 N 1379 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8037 Number of models: 1 Model: "" Number of chains: 7 Chain: "O" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "P" Number of atoms: 3798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3798 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 452} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 929 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 9} Chain: "J" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "i" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "j" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 1.56, per 1000 atoms: 0.19 Number of scatterers: 8037 At special positions: 0 Unit cell: (115.54, 109.18, 91.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 40 15.00 O 1584 8.00 N 1379 7.00 C 4989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 391.3 milliseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.4% alpha, 19.8% beta 20 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'O' and resid 37 through 46 removed outlier: 3.895A pdb=" N VAL O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 64 removed outlier: 3.974A pdb=" N TYR O 54 " --> pdb=" O PRO O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 77 Processing helix chain 'O' and resid 82 through 88 removed outlier: 3.500A pdb=" N ILE O 86 " --> pdb=" O GLY O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 176 removed outlier: 3.785A pdb=" N LYS O 174 " --> pdb=" O THR O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 200 Processing helix chain 'O' and resid 207 through 217 Processing helix chain 'O' and resid 244 through 257 Processing helix chain 'O' and resid 260 through 268 Processing helix chain 'O' and resid 268 through 284 Processing helix chain 'O' and resid 286 through 301 removed outlier: 4.404A pdb=" N GLY O 290 " --> pdb=" O ASP O 286 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 304 No H-bonds generated for 'chain 'O' and resid 302 through 304' Processing helix chain 'O' and resid 305 through 320 Proline residue: O 314 - end of helix Processing helix chain 'O' and resid 322 through 335 Processing helix chain 'P' and resid 155 through 172 Processing helix chain 'P' and resid 222 through 233 Processing helix chain 'P' and resid 234 through 248 removed outlier: 3.532A pdb=" N LYS P 246 " --> pdb=" O MET P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 278 removed outlier: 3.868A pdb=" N ALA P 278 " --> pdb=" O ASP P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 296 removed outlier: 3.559A pdb=" N MET P 286 " --> pdb=" O GLY P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 334 removed outlier: 3.583A pdb=" N LEU P 314 " --> pdb=" O THR P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 353 removed outlier: 4.088A pdb=" N GLN P 347 " --> pdb=" O HIS P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 376 Processing helix chain 'P' and resid 398 through 403 removed outlier: 3.764A pdb=" N ALA P 402 " --> pdb=" O GLY P 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 421 through 429 removed outlier: 3.745A pdb=" N ILE P 425 " --> pdb=" O ASN P 421 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 442 removed outlier: 3.575A pdb=" N GLY P 441 " --> pdb=" O PRO P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 459 removed outlier: 3.588A pdb=" N SER P 457 " --> pdb=" O MET P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 462 No H-bonds generated for 'chain 'P' and resid 460 through 462' Processing helix chain 'P' and resid 511 through 515 Processing helix chain 'P' and resid 550 through 552 No H-bonds generated for 'chain 'P' and resid 550 through 552' Processing helix chain 'R' and resid 155 through 172 Processing sheet with id=AA1, first strand: chain 'O' and resid 79 through 80 removed outlier: 6.690A pdb=" N MET O 129 " --> pdb=" O ILE O 118 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE O 120 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR O 127 " --> pdb=" O ILE O 120 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR O 142 " --> pdb=" O PHE O 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 92 through 94 removed outlier: 3.711A pdb=" N GLY P 139 " --> pdb=" O TYR P 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 92 through 94 removed outlier: 4.695A pdb=" N MET P 105 " --> pdb=" O LEU P 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'P' and resid 354 through 358 removed outlier: 5.159A pdb=" N MET P 386 " --> pdb=" O ASN P 565 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN P 565 " --> pdb=" O MET P 386 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU P 388 " --> pdb=" O GLN P 563 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN P 563 " --> pdb=" O LEU P 388 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG P 557 " --> pdb=" O VAL P 394 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS P 396 " --> pdb=" O ARG P 555 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ARG P 555 " --> pdb=" O LYS P 396 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU P 474 " --> pdb=" O ARG P 557 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU P 559 " --> pdb=" O LEU P 472 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU P 472 " --> pdb=" O LEU P 559 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS P 561 " --> pdb=" O GLY P 470 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY P 470 " --> pdb=" O LYS P 561 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU P 471 " --> pdb=" O SER P 417 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER P 417 " --> pdb=" O LEU P 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 448 through 450 removed outlier: 5.852A pdb=" N ASN P 483 " --> pdb=" O LYS P 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 529 through 530 removed outlier: 6.758A pdb=" N TYR P 543 " --> pdb=" O LYS P 507 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA P 509 " --> pdb=" O TYR P 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 516 through 518 Processing sheet with id=AA9, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.833A pdb=" N HIS R 93 " --> pdb=" O GLU R 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 132 " --> pdb=" O CYS R 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.833A pdb=" N HIS R 93 " --> pdb=" O GLU R 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 96 through 97 332 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2121 1.33 - 1.45: 1667 1.45 - 1.57: 4354 1.57 - 1.69: 76 1.69 - 1.81: 73 Bond restraints: 8291 Sorted by residual: bond pdb=" C1' DT i 78 " pdb=" N1 DT i 78 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.69e+01 bond pdb=" C1' DT j -82 " pdb=" N1 DT j -82 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.48e+01 bond pdb=" C1' DA i 82 " pdb=" N9 DA i 82 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.44e+01 bond pdb=" C1' DA j -81 " pdb=" N9 DA j -81 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.29e+01 bond pdb=" C1' DT i 81 " pdb=" N1 DT i 81 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.87e+01 ... (remaining 8286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 10834 1.88 - 3.76: 455 3.76 - 5.64: 48 5.64 - 7.52: 13 7.52 - 9.40: 2 Bond angle restraints: 11352 Sorted by residual: angle pdb=" O4' DT i 81 " pdb=" C1' DT i 81 " pdb=" N1 DT i 81 " ideal model delta sigma weight residual 108.00 113.05 -5.05 7.00e-01 2.04e+00 5.20e+01 angle pdb=" O4' DT J 77 " pdb=" C1' DT J 77 " pdb=" N1 DT J 77 " ideal model delta sigma weight residual 108.00 111.84 -3.84 7.00e-01 2.04e+00 3.01e+01 angle pdb=" O5' DT J 82 " pdb=" C5' DT J 82 " pdb=" C4' DT J 82 " ideal model delta sigma weight residual 109.40 113.42 -4.02 8.00e-01 1.56e+00 2.53e+01 angle pdb=" N3 DT I -80 " pdb=" C4 DT I -80 " pdb=" O4 DT I -80 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" O4 DT I -80 " pdb=" C4 DT I -80 " pdb=" C5 DT I -80 " ideal model delta sigma weight residual 124.90 121.87 3.03 7.00e-01 2.04e+00 1.87e+01 ... (remaining 11347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 4630 34.73 - 69.46: 260 69.46 - 104.19: 10 104.19 - 138.92: 0 138.92 - 173.64: 1 Dihedral angle restraints: 4901 sinusoidal: 2294 harmonic: 2607 Sorted by residual: dihedral pdb=" CA GLY R 90 " pdb=" C GLY R 90 " pdb=" N LYS R 91 " pdb=" CA LYS R 91 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN P 99 " pdb=" C ASN P 99 " pdb=" N ASP P 100 " pdb=" CA ASP P 100 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" C4' DA J 80 " pdb=" C3' DA J 80 " pdb=" O3' DA J 80 " pdb=" P DT J 81 " ideal model delta sinusoidal sigma weight residual 220.00 46.36 173.64 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 4898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 871 0.051 - 0.101: 270 0.101 - 0.152: 71 0.152 - 0.202: 5 0.202 - 0.253: 3 Chirality restraints: 1220 Sorted by residual: chirality pdb=" C3' DA J 80 " pdb=" C4' DA J 80 " pdb=" O3' DA J 80 " pdb=" C2' DA J 80 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE O 182 " pdb=" N ILE O 182 " pdb=" C ILE O 182 " pdb=" CB ILE O 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1' DA i 82 " pdb=" O4' DA i 82 " pdb=" C2' DA i 82 " pdb=" N9 DA i 82 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1217 not shown) Planarity restraints: 1329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 425 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ILE P 425 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE P 425 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU P 426 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA i 80 " -0.032 2.00e-02 2.50e+03 1.39e-02 5.29e+00 pdb=" N9 DA i 80 " 0.006 2.00e-02 2.50e+03 pdb=" C8 DA i 80 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA i 80 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA i 80 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DA i 80 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA i 80 " -0.024 2.00e-02 2.50e+03 pdb=" N1 DA i 80 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA i 80 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA i 80 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA i 80 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT j -82 " 0.024 2.00e-02 2.50e+03 1.22e-02 3.73e+00 pdb=" N1 DT j -82 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT j -82 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT j -82 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DT j -82 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT j -82 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT j -82 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT j -82 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT j -82 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT j -82 " -0.015 2.00e-02 2.50e+03 ... (remaining 1326 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 125 2.63 - 3.20: 7616 3.20 - 3.77: 13417 3.77 - 4.33: 17912 4.33 - 4.90: 27606 Nonbonded interactions: 66676 Sorted by model distance: nonbonded pdb=" C2' DA i 77 " pdb=" C7 DT i 78 " model vdw 2.067 3.860 nonbonded pdb=" OE2 GLU O 114 " pdb=" OH TYR O 317 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR P 119 " pdb=" OP1 DT j -82 " model vdw 2.119 3.040 nonbonded pdb=" OH TYR O 109 " pdb=" O GLY O 301 " model vdw 2.161 3.040 nonbonded pdb=" N GLY P 506 " pdb=" OD1 ASN P 544 " model vdw 2.174 3.120 ... (remaining 66671 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 group one per residue 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: 10.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.710 Find NCS groups from input model: 0.070 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 8291 Z= 0.396 Angle : 0.874 9.403 11352 Z= 0.569 Chirality : 0.052 0.253 1220 Planarity : 0.005 0.035 1329 Dihedral : 18.875 173.644 3223 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.26), residues: 884 helix: -0.58 (0.26), residues: 317 sheet: -0.40 (0.40), residues: 157 loop : -1.62 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 140 TYR 0.023 0.002 TYR P 188 PHE 0.019 0.003 PHE P 113 TRP 0.022 0.003 TRP P 135 HIS 0.009 0.002 HIS O 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.40 ( 8291) covalent geometry : angle 0.87449 / 0.57 (11352) hydrogen bonds : bond 0.14647 / 9.04 ( 378) hydrogen bonds : angle 7.01309 / 4.87 ( 1040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: O 239 ARG cc_start: 0.7160 (ptp-170) cc_final: 0.6849 (ptp-110) REVERT: O 305 PHE cc_start: 0.6355 (m-10) cc_final: 0.6062 (m-10) REVERT: O 311 GLN cc_start: 0.7774 (mt0) cc_final: 0.7545 (mt0) REVERT: O 327 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7440 (mm-30) REVERT: P 108 GLN cc_start: 0.7620 (tt0) cc_final: 0.7271 (tm-30) REVERT: P 241 MET cc_start: 0.7810 (tpt) cc_final: 0.7350 (tpt) REVERT: P 290 ASN cc_start: 0.7103 (m110) cc_final: 0.5829 (m110) REVERT: P 468 ASN cc_start: 0.6550 (p0) cc_final: 0.6345 (p0) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.0943 time to fit residues: 22.2582 Evaluate side-chains 110 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 290 ASN ** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 553 GLN ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.106811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.098554 restraints weight = 32456.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.100099 restraints weight = 18881.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.101140 restraints weight = 12268.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.101860 restraints weight = 8784.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.102387 restraints weight = 6754.489| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8291 Z= 0.169 Angle : 0.756 9.501 11352 Z= 0.401 Chirality : 0.047 0.317 1220 Planarity : 0.004 0.033 1329 Dihedral : 20.014 165.671 1394 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.91 % Allowed : 12.24 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.31 (0.27), residues: 884 helix: 0.60 (0.27), residues: 321 sheet: -0.12 (0.40), residues: 144 loop : -0.81 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 140 TYR 0.024 0.002 TYR O 317 PHE 0.025 0.003 PHE R 132 TRP 0.027 0.003 TRP O 57 HIS 0.008 0.001 HIS O 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 8291) covalent geometry : angle 0.75586 / 0.40 (11352) hydrogen bonds : bond 0.05230 / 3.30 ( 378) hydrogen bonds : angle 5.88574 / 3.99 ( 1040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 222 PHE cc_start: 0.6208 (m-10) cc_final: 0.5759 (m-10) REVERT: O 239 ARG cc_start: 0.7182 (ptp-170) cc_final: 0.6568 (ptp-110) REVERT: O 289 MET cc_start: 0.7000 (ttm) cc_final: 0.6658 (ttm) REVERT: O 311 GLN cc_start: 0.7751 (mt0) cc_final: 0.7493 (mt0) REVERT: P 108 GLN cc_start: 0.7581 (tt0) cc_final: 0.7363 (tm-30) REVERT: R 124 LEU cc_start: 0.7854 (mm) cc_final: 0.7241 (tp) REVERT: R 134 VAL cc_start: 0.7654 (t) cc_final: 0.7008 (t) REVERT: R 135 TRP cc_start: 0.6528 (t-100) cc_final: 0.6118 (t-100) REVERT: R 136 MET cc_start: 0.7402 (mpp) cc_final: 0.6246 (mtp) outliers start: 15 outliers final: 11 residues processed: 133 average time/residue: 0.0787 time to fit residues: 14.6984 Evaluate side-chains 120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 254 LEU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 123 ASN ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 303 HIS P 147 HIS ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 267 GLN ** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 ASN P 519 ASN ** P 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.103704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.095537 restraints weight = 32621.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.097012 restraints weight = 19028.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.098059 restraints weight = 12585.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.098767 restraints weight = 8930.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.099280 restraints weight = 6848.198| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8291 Z= 0.238 Angle : 0.784 10.199 11352 Z= 0.417 Chirality : 0.048 0.304 1220 Planarity : 0.004 0.042 1329 Dihedral : 19.918 163.200 1394 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.44 % Allowed : 15.31 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.36 (0.27), residues: 884 helix: 0.51 (0.27), residues: 320 sheet: -0.25 (0.40), residues: 161 loop : -0.75 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 107 TYR 0.030 0.002 TYR O 317 PHE 0.029 0.003 PHE O 305 TRP 0.020 0.003 TRP P 414 HIS 0.006 0.002 HIS P 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 ( 8291) covalent geometry : angle 0.78415 / 0.42 (11352) hydrogen bonds : bond 0.05412 / 3.52 ( 378) hydrogen bonds : angle 5.84763 / 3.99 ( 1040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: O 141 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7068 (t) REVERT: O 239 ARG cc_start: 0.7527 (ptp-170) cc_final: 0.7242 (ptp-110) REVERT: O 295 MET cc_start: 0.6895 (tpt) cc_final: 0.6289 (tpt) REVERT: O 311 GLN cc_start: 0.7752 (mt0) cc_final: 0.7390 (mt0) REVERT: P 108 GLN cc_start: 0.7747 (tt0) cc_final: 0.7414 (tm-30) REVERT: P 251 LYS cc_start: 0.8144 (tptm) cc_final: 0.7871 (tptm) REVERT: P 290 ASN cc_start: 0.7133 (m-40) cc_final: 0.6857 (m110) REVERT: P 419 MET cc_start: 0.7493 (tpp) cc_final: 0.7177 (tpp) REVERT: R 105 MET cc_start: 0.8243 (tpp) cc_final: 0.7438 (tpt) REVERT: R 134 VAL cc_start: 0.7799 (t) cc_final: 0.7109 (t) REVERT: R 135 TRP cc_start: 0.6719 (t-100) cc_final: 0.6273 (t-100) REVERT: R 136 MET cc_start: 0.7504 (mpp) cc_final: 0.6317 (mtp) outliers start: 27 outliers final: 17 residues processed: 129 average time/residue: 0.0723 time to fit residues: 13.1095 Evaluate side-chains 118 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 195 TYR Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 443 MET Chi-restraints excluded: chain P residue 468 ASN Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.0050 chunk 79 optimal weight: 3.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 ASN P 226 GLN ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.105682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.097495 restraints weight = 32677.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.099002 restraints weight = 18946.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.100057 restraints weight = 12401.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.100787 restraints weight = 8779.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.101238 restraints weight = 6667.590| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8291 Z= 0.142 Angle : 0.704 12.292 11352 Z= 0.370 Chirality : 0.045 0.288 1220 Planarity : 0.003 0.030 1329 Dihedral : 19.862 163.059 1394 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.19 % Allowed : 17.35 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.01 (0.28), residues: 884 helix: 0.77 (0.28), residues: 320 sheet: -0.01 (0.42), residues: 158 loop : -0.54 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 140 TYR 0.024 0.001 TYR O 317 PHE 0.025 0.002 PHE O 305 TRP 0.021 0.002 TRP P 414 HIS 0.004 0.001 HIS O 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 8291) covalent geometry : angle 0.70419 / 0.37 (11352) hydrogen bonds : bond 0.04432 / 2.87 ( 378) hydrogen bonds : angle 5.56205 / 3.78 ( 1040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 239 ARG cc_start: 0.7361 (ptp-170) cc_final: 0.6884 (ptp-110) REVERT: O 257 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: O 311 GLN cc_start: 0.7679 (mt0) cc_final: 0.7384 (mt0) REVERT: P 108 GLN cc_start: 0.7696 (tt0) cc_final: 0.7396 (tm-30) REVERT: P 144 MET cc_start: 0.7770 (tmm) cc_final: 0.7362 (tmm) REVERT: P 251 LYS cc_start: 0.8103 (tptm) cc_final: 0.7901 (tptm) REVERT: P 290 ASN cc_start: 0.7081 (m-40) cc_final: 0.6820 (m110) REVERT: P 419 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7374 (tpp) outliers start: 25 outliers final: 16 residues processed: 126 average time/residue: 0.0719 time to fit residues: 12.8463 Evaluate side-chains 120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 174 LYS Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 419 MET Chi-restraints excluded: chain P residue 468 ASN Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** 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 = 0.3917 r_free = 0.3917 target = 0.103010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.094687 restraints weight = 32987.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.096177 restraints weight = 19407.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.097202 restraints weight = 12765.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.097931 restraints weight = 9151.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.098435 restraints weight = 7012.176| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8291 Z= 0.224 Angle : 0.757 10.755 11352 Z= 0.400 Chirality : 0.048 0.288 1220 Planarity : 0.004 0.049 1329 Dihedral : 19.869 161.440 1394 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.21 % Allowed : 17.35 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.19 (0.28), residues: 884 helix: 0.67 (0.29), residues: 321 sheet: -0.17 (0.42), residues: 160 loop : -0.68 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 295 TYR 0.031 0.002 TYR O 317 PHE 0.025 0.003 PHE O 305 TRP 0.024 0.003 TRP P 414 HIS 0.005 0.001 HIS O 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 ( 8291) covalent geometry : angle 0.75682 / 0.40 (11352) hydrogen bonds : bond 0.04971 / 3.25 ( 378) hydrogen bonds : angle 5.65152 / 3.86 ( 1040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: O 239 ARG cc_start: 0.7478 (ptp-170) cc_final: 0.7229 (ptp90) REVERT: O 275 MET cc_start: 0.7423 (mmp) cc_final: 0.7153 (mmp) REVERT: O 311 GLN cc_start: 0.7604 (mt0) cc_final: 0.7336 (mt0) REVERT: O 317 TYR cc_start: 0.6958 (m-80) cc_final: 0.6661 (m-80) REVERT: P 108 GLN cc_start: 0.7851 (tt0) cc_final: 0.7401 (tm-30) REVERT: P 144 MET cc_start: 0.7733 (tmm) cc_final: 0.6860 (tmm) REVERT: P 251 LYS cc_start: 0.8232 (tptm) cc_final: 0.8026 (tptm) REVERT: P 290 ASN cc_start: 0.7169 (m-40) cc_final: 0.6967 (m110) REVERT: P 419 MET cc_start: 0.7648 (tpp) cc_final: 0.7395 (tpp) REVERT: P 453 MET cc_start: 0.7648 (mmp) cc_final: 0.6908 (mtm) outliers start: 33 outliers final: 22 residues processed: 120 average time/residue: 0.0782 time to fit residues: 13.3889 Evaluate side-chains 116 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 195 TYR Chi-restraints excluded: chain P residue 225 VAL Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 443 MET Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 5 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 ASN ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.105650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.097258 restraints weight = 32265.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.098759 restraints weight = 19212.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.099810 restraints weight = 12779.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.100548 restraints weight = 9202.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.101030 restraints weight = 7068.956| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8291 Z= 0.134 Angle : 0.712 12.756 11352 Z= 0.364 Chirality : 0.045 0.276 1220 Planarity : 0.003 0.026 1329 Dihedral : 19.770 161.766 1394 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.19 % Allowed : 19.01 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.03 (0.28), residues: 884 helix: 0.85 (0.29), residues: 320 sheet: 0.11 (0.44), residues: 154 loop : -0.61 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 140 TYR 0.030 0.002 TYR O 317 PHE 0.026 0.002 PHE O 305 TRP 0.031 0.002 TRP P 414 HIS 0.004 0.001 HIS O 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 8291) covalent geometry : angle 0.71183 / 0.36 (11352) hydrogen bonds : bond 0.04079 / 2.66 ( 378) hydrogen bonds : angle 5.40539 / 3.67 ( 1040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: O 275 MET cc_start: 0.7873 (mmp) cc_final: 0.7403 (mmp) REVERT: O 311 GLN cc_start: 0.7548 (mt0) cc_final: 0.7210 (mt0) REVERT: P 108 GLN cc_start: 0.7731 (tt0) cc_final: 0.7362 (tm-30) REVERT: P 144 MET cc_start: 0.7773 (tmm) cc_final: 0.7280 (tmm) REVERT: P 270 LYS cc_start: 0.7840 (tppt) cc_final: 0.7422 (tptt) REVERT: P 290 ASN cc_start: 0.7115 (m-40) cc_final: 0.6885 (m110) REVERT: R 136 MET cc_start: 0.7575 (mpp) cc_final: 0.6138 (mtp) outliers start: 25 outliers final: 18 residues processed: 124 average time/residue: 0.0747 time to fit residues: 13.3374 Evaluate side-chains 114 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 299 CYS Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 72 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 377 HIS P 428 HIS ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.105736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.097313 restraints weight = 32762.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.098841 restraints weight = 19385.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.099909 restraints weight = 12841.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.100672 restraints weight = 9176.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.101141 restraints weight = 7000.235| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8291 Z= 0.132 Angle : 0.707 12.274 11352 Z= 0.363 Chirality : 0.045 0.274 1220 Planarity : 0.004 0.042 1329 Dihedral : 19.673 162.462 1394 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.68 % Allowed : 21.43 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.04 (0.28), residues: 884 helix: 0.88 (0.29), residues: 322 sheet: 0.16 (0.43), residues: 154 loop : -0.66 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 140 TYR 0.040 0.002 TYR O 317 PHE 0.024 0.002 PHE O 305 TRP 0.035 0.002 TRP P 414 HIS 0.006 0.001 HIS O 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8291) covalent geometry : angle 0.70716 / 0.36 (11352) hydrogen bonds : bond 0.04058 / 2.66 ( 378) hydrogen bonds : angle 5.35715 / 3.64 ( 1040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: O 311 GLN cc_start: 0.7529 (mt0) cc_final: 0.7144 (mt0) REVERT: P 108 GLN cc_start: 0.7769 (tt0) cc_final: 0.7364 (tm-30) REVERT: P 144 MET cc_start: 0.7731 (tmm) cc_final: 0.7352 (tmm) REVERT: P 270 LYS cc_start: 0.7823 (tppt) cc_final: 0.7443 (tptt) REVERT: P 453 MET cc_start: 0.7429 (mmp) cc_final: 0.6879 (mtm) REVERT: R 105 MET cc_start: 0.8076 (tpp) cc_final: 0.7545 (tpp) REVERT: R 132 PHE cc_start: 0.3802 (m-80) cc_final: 0.3553 (m-10) REVERT: R 136 MET cc_start: 0.7556 (mpp) cc_final: 0.6239 (mtp) outliers start: 21 outliers final: 18 residues processed: 114 average time/residue: 0.0751 time to fit residues: 12.0047 Evaluate side-chains 115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 248 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** 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 = 0.3949 r_free = 0.3949 target = 0.104818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.096477 restraints weight = 32233.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.097935 restraints weight = 19017.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.099005 restraints weight = 12624.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.099764 restraints weight = 8974.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.100286 restraints weight = 6826.484| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8291 Z= 0.158 Angle : 0.722 12.405 11352 Z= 0.371 Chirality : 0.045 0.276 1220 Planarity : 0.004 0.047 1329 Dihedral : 19.659 162.227 1394 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.93 % Allowed : 21.81 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.06 (0.29), residues: 884 helix: 0.79 (0.29), residues: 323 sheet: -0.04 (0.44), residues: 150 loop : -0.64 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 140 TYR 0.034 0.002 TYR O 317 PHE 0.020 0.002 PHE O 305 TRP 0.035 0.002 TRP P 414 HIS 0.003 0.001 HIS O 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 8291) covalent geometry : angle 0.72166 / 0.37 (11352) hydrogen bonds : bond 0.04157 / 2.75 ( 378) hydrogen bonds : angle 5.42899 / 3.73 ( 1040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 239 ARG cc_start: 0.7540 (ptp90) cc_final: 0.7271 (ptp-170) REVERT: O 268 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: O 289 MET cc_start: 0.7129 (ttm) cc_final: 0.6652 (ttm) REVERT: O 295 MET cc_start: 0.6770 (tpp) cc_final: 0.6569 (tpp) REVERT: O 311 GLN cc_start: 0.7430 (mt0) cc_final: 0.7017 (mt0) REVERT: P 108 GLN cc_start: 0.7793 (tt0) cc_final: 0.7348 (tm-30) REVERT: P 144 MET cc_start: 0.7820 (tmm) cc_final: 0.7329 (tmm) REVERT: P 270 LYS cc_start: 0.7755 (tppt) cc_final: 0.7365 (tptt) REVERT: P 453 MET cc_start: 0.7557 (mmp) cc_final: 0.6911 (mtm) REVERT: R 136 MET cc_start: 0.7587 (mpp) cc_final: 0.6325 (mtt) outliers start: 23 outliers final: 20 residues processed: 112 average time/residue: 0.0764 time to fit residues: 12.2903 Evaluate side-chains 115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 248 LEU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain P residue 519 ASN Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 541 LEU Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 ASN ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.105280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.096967 restraints weight = 32128.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.098451 restraints weight = 18908.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.099538 restraints weight = 12467.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100285 restraints weight = 8832.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.100806 restraints weight = 6688.139| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8291 Z= 0.139 Angle : 0.727 13.975 11352 Z= 0.369 Chirality : 0.045 0.276 1220 Planarity : 0.003 0.036 1329 Dihedral : 19.636 162.565 1394 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.93 % Allowed : 22.45 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.29), residues: 884 helix: 0.87 (0.29), residues: 323 sheet: -0.04 (0.44), residues: 150 loop : -0.62 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 140 TYR 0.027 0.002 TYR O 317 PHE 0.019 0.002 PHE O 305 TRP 0.041 0.002 TRP P 414 HIS 0.004 0.001 HIS O 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 8291) covalent geometry : angle 0.72665 / 0.37 (11352) hydrogen bonds : bond 0.04051 / 2.65 ( 378) hydrogen bonds : angle 5.35326 / 3.67 ( 1040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: O 239 ARG cc_start: 0.7556 (ptp90) cc_final: 0.7303 (ptp-170) REVERT: O 268 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6708 (m-80) REVERT: O 289 MET cc_start: 0.7230 (ttm) cc_final: 0.6850 (ttm) REVERT: O 295 MET cc_start: 0.6783 (tpp) cc_final: 0.6409 (tpt) REVERT: O 311 GLN cc_start: 0.7481 (mt0) cc_final: 0.7070 (mt0) REVERT: P 108 GLN cc_start: 0.7783 (tt0) cc_final: 0.7251 (tm-30) REVERT: P 144 MET cc_start: 0.7766 (tmm) cc_final: 0.7274 (tmm) REVERT: P 270 LYS cc_start: 0.7762 (tppt) cc_final: 0.7339 (tptt) REVERT: P 453 MET cc_start: 0.7509 (mmp) cc_final: 0.6865 (mtm) REVERT: R 105 MET cc_start: 0.8139 (tpp) cc_final: 0.7499 (tpp) REVERT: R 136 MET cc_start: 0.7580 (mpp) cc_final: 0.6349 (mtp) outliers start: 23 outliers final: 18 residues processed: 115 average time/residue: 0.0778 time to fit residues: 12.7788 Evaluate side-chains 114 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain P residue 519 ASN Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.106524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.098235 restraints weight = 32278.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.099789 restraints weight = 19072.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.100842 restraints weight = 12440.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101584 restraints weight = 8872.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.102097 restraints weight = 6777.825| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8291 Z= 0.128 Angle : 0.705 13.369 11352 Z= 0.358 Chirality : 0.044 0.278 1220 Planarity : 0.003 0.029 1329 Dihedral : 19.548 163.369 1394 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.55 % Allowed : 22.45 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.09 (0.28), residues: 884 helix: 0.96 (0.29), residues: 323 sheet: 0.06 (0.43), residues: 150 loop : -0.60 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.022 0.001 TYR O 317 PHE 0.023 0.002 PHE R 132 TRP 0.049 0.002 TRP P 414 HIS 0.003 0.001 HIS O 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 8291) covalent geometry : angle 0.70467 / 0.36 (11352) hydrogen bonds : bond 0.03863 / 2.53 ( 378) hydrogen bonds : angle 5.28245 / 3.63 ( 1040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: O 239 ARG cc_start: 0.7562 (ptp90) cc_final: 0.7330 (ptp-170) REVERT: O 268 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: O 289 MET cc_start: 0.7168 (ttm) cc_final: 0.6709 (ttm) REVERT: O 311 GLN cc_start: 0.7456 (mt0) cc_final: 0.6983 (mt0) REVERT: P 108 GLN cc_start: 0.7767 (tt0) cc_final: 0.7211 (tm-30) REVERT: P 144 MET cc_start: 0.7726 (tmm) cc_final: 0.7351 (tmm) REVERT: P 270 LYS cc_start: 0.7722 (tppt) cc_final: 0.7294 (tptt) REVERT: P 419 MET cc_start: 0.8159 (tpp) cc_final: 0.7531 (tpp) REVERT: P 453 MET cc_start: 0.7484 (mmp) cc_final: 0.6867 (mtm) REVERT: R 89 VAL cc_start: 0.6554 (OUTLIER) cc_final: 0.6327 (m) REVERT: R 105 MET cc_start: 0.8122 (tpp) cc_final: 0.7524 (tpp) REVERT: R 136 MET cc_start: 0.7539 (mpp) cc_final: 0.6364 (mtp) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 0.0770 time to fit residues: 12.6865 Evaluate side-chains 112 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 219 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 268 PHE Chi-restraints excluded: chain O residue 320 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 146 GLN Chi-restraints excluded: chain P residue 179 GLU Chi-restraints excluded: chain P residue 353 HIS Chi-restraints excluded: chain P residue 477 VAL Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain P residue 519 ASN Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain P residue 556 MET Chi-restraints excluded: chain P residue 567 LEU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 180 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 0 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** 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 = 0.3920 r_free = 0.3920 target = 0.103264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.095075 restraints weight = 32499.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.096535 restraints weight = 19233.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.097580 restraints weight = 12699.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.098262 restraints weight = 9100.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.098776 restraints weight = 7030.632| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8291 Z= 0.205 Angle : 0.764 12.048 11352 Z= 0.395 Chirality : 0.047 0.276 1220 Planarity : 0.004 0.043 1329 Dihedral : 19.644 163.021 1394 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.42 % Allowed : 23.09 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.06 (0.29), residues: 884 helix: 0.70 (0.29), residues: 322 sheet: -0.04 (0.44), residues: 148 loop : -0.55 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 213 TYR 0.038 0.002 TYR O 317 PHE 0.017 0.002 PHE O 305 TRP 0.054 0.003 TRP P 414 HIS 0.005 0.001 HIS O 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 8291) covalent geometry : angle 0.76418 / 0.39 (11352) hydrogen bonds : bond 0.04563 / 2.99 ( 378) hydrogen bonds : angle 5.47582 / 3.78 ( 1040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1376.79 seconds wall clock time: 24 minutes 39.65 seconds (1479.65 seconds total)