Starting phenix.real_space_refine on Sun Aug 24 05:54:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf3_45528/08_2025/9cf3_45528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf3_45528/08_2025/9cf3_45528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2025/9cf3_45528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2025/9cf3_45528.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2025/9cf3_45528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf3_45528/08_2025/9cf3_45528.map" } resolution = 3.2 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= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 98 5.49 5 S 35 5.16 5 C 5573 2.51 5 N 1629 2.21 5 O 1933 1.98 5 H 8383 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17651 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2426 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 151} Chain: "N" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 350 Classifications: {'DNA': 11} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 12097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 12097 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 26, 'TRANS': 699} Chain breaks: 1 Chain: "T" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 991 Classifications: {'DNA': 31} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "W" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1787 Classifications: {'DNA': 15, 'RNA': 41} Modifications used: {'3*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 16} Link IDs: {'rna2p': 7, 'rna3p': 48} Time building chain proxies: 2.77, per 1000 atoms: 0.16 Number of scatterers: 17651 At special positions: 0 Unit cell: (81.675, 119.625, 123.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 98 15.00 O 1933 8.00 N 1629 7.00 C 5573 6.00 H 8383 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 396.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 51.9% alpha, 12.3% beta 36 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.647A pdb=" N LEU B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 119 through 121 No H-bonds generated for 'chain 'P' and resid 119 through 121' Processing helix chain 'P' and resid 122 through 155 removed outlier: 3.662A pdb=" N LEU P 126 " --> pdb=" O TYR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 164 removed outlier: 3.542A pdb=" N ILE P 164 " --> pdb=" O ASN P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.637A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 removed outlier: 3.669A pdb=" N ARG P 186 " --> pdb=" O ASN P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 210 removed outlier: 3.974A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 255 removed outlier: 3.545A pdb=" N ALA P 228 " --> pdb=" O LEU P 224 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN P 244 " --> pdb=" O ALA P 240 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG P 245 " --> pdb=" O HIS P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 270 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 285 through 298 Processing helix chain 'P' and resid 308 through 320 Processing helix chain 'P' and resid 332 through 340 removed outlier: 3.866A pdb=" N VAL P 338 " --> pdb=" O PHE P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 344 through 358 Processing helix chain 'P' and resid 381 through 388 removed outlier: 4.311A pdb=" N TYR P 386 " --> pdb=" O LYS P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 398 No H-bonds generated for 'chain 'P' and resid 396 through 398' Processing helix chain 'P' and resid 399 through 406 removed outlier: 3.586A pdb=" N ARG P 406 " --> pdb=" O ASN P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 419 through 423 Processing helix chain 'P' and resid 466 through 470 Processing helix chain 'P' and resid 471 through 476 Processing helix chain 'P' and resid 477 through 479 No H-bonds generated for 'chain 'P' and resid 477 through 479' Processing helix chain 'P' and resid 512 through 516 Processing helix chain 'P' and resid 516 through 529 Processing helix chain 'P' and resid 531 through 542 Processing helix chain 'P' and resid 550 through 574 removed outlier: 3.523A pdb=" N VAL P 564 " --> pdb=" O ALA P 560 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 622 through 628 removed outlier: 3.714A pdb=" N LYS P 626 " --> pdb=" O ASP P 622 " (cutoff:3.500A) Processing helix chain 'P' and resid 628 through 639 removed outlier: 4.016A pdb=" N THR P 632 " --> pdb=" O HIS P 628 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 Processing helix chain 'P' and resid 648 through 665 Processing helix chain 'P' and resid 668 through 679 removed outlier: 3.891A pdb=" N LYS P 672 " --> pdb=" O GLU P 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 680 through 684 Processing helix chain 'P' and resid 686 through 713 Processing helix chain 'P' and resid 738 through 747 Processing helix chain 'P' and resid 780 through 786 removed outlier: 3.879A pdb=" N GLU P 785 " --> pdb=" O HIS P 782 " (cutoff:3.500A) Processing helix chain 'P' and resid 800 through 804 removed outlier: 3.994A pdb=" N LEU P 804 " --> pdb=" O MET P 801 " (cutoff:3.500A) Processing helix chain 'P' and resid 818 through 837 Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.797A pdb=" N ARG B 53 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLN B 109 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 128 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N MET B 98 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 126 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 16 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL B 156 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 107 through 113 removed outlier: 3.513A pdb=" N LEU P 440 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLN P 442 " --> pdb=" O GLN P 427 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN P 427 " --> pdb=" O GLN P 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'P' and resid 507 through 511 removed outlier: 5.918A pdb=" N VAL P 483 " --> pdb=" O VAL P 720 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY P 722 " --> pdb=" O VAL P 483 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N MET P 485 " --> pdb=" O GLY P 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 591 through 593 removed outlier: 3.522A pdb=" N ALA P 607 " --> pdb=" O LEU P 599 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR P 601 " --> pdb=" O PHE P 605 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE P 605 " --> pdb=" O TYR P 601 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 770 through 772 Processing sheet with id=AA7, first strand: chain 'P' and resid 775 through 777 342 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8366 1.03 - 1.23: 53 1.23 - 1.42: 4148 1.42 - 1.62: 5433 1.62 - 1.81: 53 Bond restraints: 18053 Sorted by residual: bond pdb=" O5' U W 30 " pdb=" C5' U W 30 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.72e+00 bond pdb=" C1' A W 32 " pdb=" N9 A W 32 " ideal model delta sigma weight residual 1.475 1.493 -0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" O5' A W 33 " pdb=" C5' A W 33 " ideal model delta sigma weight residual 1.420 1.437 -0.017 1.50e-02 4.44e+03 1.30e+00 bond pdb=" C1' A W 7 " pdb=" N9 A W 7 " ideal model delta sigma weight residual 1.465 1.481 -0.016 1.50e-02 4.44e+03 1.15e+00 bond pdb=" CA ILE P 609 " pdb=" CB ILE P 609 " ideal model delta sigma weight residual 1.530 1.541 -0.010 1.05e-02 9.07e+03 9.63e-01 ... (remaining 18048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 32376 2.37 - 4.75: 229 4.75 - 7.12: 9 7.12 - 9.49: 9 9.49 - 11.86: 19 Bond angle restraints: 32642 Sorted by residual: angle pdb=" O4' U W 30 " pdb=" C1' U W 30 " pdb=" N1 U W 30 " ideal model delta sigma weight residual 108.50 117.35 -8.85 1.50e+00 4.44e-01 3.48e+01 angle pdb=" P A W 33 " pdb=" O5' A W 33 " pdb=" C5' A W 33 " ideal model delta sigma weight residual 120.90 128.18 -7.28 1.50e+00 4.44e-01 2.36e+01 angle pdb=" C2' A W 32 " pdb=" C1' A W 32 " pdb=" N9 A W 32 " ideal model delta sigma weight residual 112.00 119.05 -7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" C2' U W 30 " pdb=" C1' U W 30 " pdb=" N1 U W 30 " ideal model delta sigma weight residual 112.00 118.42 -6.42 1.50e+00 4.44e-01 1.83e+01 angle pdb=" OP1 A W 29 " pdb=" P A W 29 " pdb=" OP2 A W 29 " ideal model delta sigma weight residual 119.60 107.74 11.86 3.00e+00 1.11e-01 1.56e+01 ... (remaining 32637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 7889 35.59 - 71.18: 361 71.18 - 106.78: 24 106.78 - 142.37: 9 142.37 - 177.96: 6 Dihedral angle restraints: 8289 sinusoidal: 5163 harmonic: 3126 Sorted by residual: dihedral pdb=" C4' A W 7 " pdb=" C3' A W 7 " pdb=" C2' A W 7 " pdb=" C1' A W 7 " ideal model delta sinusoidal sigma weight residual -35.00 37.48 -72.48 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C5' A W 7 " pdb=" C4' A W 7 " pdb=" C3' A W 7 " pdb=" O3' A W 7 " ideal model delta sinusoidal sigma weight residual 147.00 74.96 72.04 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" O4' A W 7 " pdb=" C4' A W 7 " pdb=" C3' A W 7 " pdb=" C2' A W 7 " ideal model delta sinusoidal sigma weight residual 24.00 -39.54 63.54 1 8.00e+00 1.56e-02 8.32e+01 ... (remaining 8286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1461 0.113 - 0.227: 20 0.227 - 0.340: 8 0.340 - 0.454: 8 0.454 - 0.567: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" C1' U W 30 " pdb=" O4' U W 30 " pdb=" C2' U W 30 " pdb=" N1 U W 30 " both_signs ideal model delta sigma weight residual False 2.47 1.90 0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" P DT N -1 " pdb=" OP1 DT N -1 " pdb=" OP2 DT N -1 " pdb=" O5' DT N -1 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" P DA T 1 " pdb=" OP1 DA T 1 " pdb=" OP2 DA T 1 " pdb=" O5' DA T 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1495 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U W 30 " 0.033 2.00e-02 2.50e+03 2.13e-02 1.36e+01 pdb=" N1 U W 30 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U W 30 " -0.032 2.00e-02 2.50e+03 pdb=" O2 U W 30 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U W 30 " 0.035 2.00e-02 2.50e+03 pdb=" C4 U W 30 " -0.028 2.00e-02 2.50e+03 pdb=" O4 U W 30 " 0.024 2.00e-02 2.50e+03 pdb=" C5 U W 30 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U W 30 " 0.001 2.00e-02 2.50e+03 pdb=" H5 U W 30 " -0.000 2.00e-02 2.50e+03 pdb=" H3 U W 30 " -0.002 2.00e-02 2.50e+03 pdb=" H6 U W 30 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A W 32 " -0.031 2.00e-02 2.50e+03 1.89e-02 1.17e+01 pdb=" N9 A W 32 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A W 32 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A W 32 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A W 32 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A W 32 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A W 32 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A W 32 " -0.039 2.00e-02 2.50e+03 pdb=" C2 A W 32 " 0.034 2.00e-02 2.50e+03 pdb=" N3 A W 32 " -0.000 2.00e-02 2.50e+03 pdb=" C4 A W 32 " -0.000 2.00e-02 2.50e+03 pdb=" H8 A W 32 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A W 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 738 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LYS P 738 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS P 738 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY P 739 " -0.013 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.88: 87 1.88 - 2.56: 14671 2.56 - 3.24: 53844 3.24 - 3.92: 66159 3.92 - 4.60: 107176 Nonbonded interactions: 241937 Sorted by model distance: nonbonded pdb="HE21 GLN P 221 " pdb=" OH TYR P 225 " model vdw 1.194 2.450 nonbonded pdb=" HG3 GLN P 221 " pdb=" CE2 TYR P 225 " model vdw 1.295 2.970 nonbonded pdb=" O THR P 759 " pdb="HD21 ASN P 825 " model vdw 1.609 2.450 nonbonded pdb=" HZ3 LYS P 400 " pdb=" O GLN P 427 " model vdw 1.611 2.450 nonbonded pdb=" O THR P 539 " pdb=" HG SER P 542 " model vdw 1.622 2.450 ... (remaining 241932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 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 : 0.002 0.029 9670 Z= 0.124 Angle : 0.717 11.863 13460 Z= 0.374 Chirality : 0.053 0.567 1498 Planarity : 0.003 0.037 1368 Dihedral : 18.408 177.959 4055 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.30), residues: 882 helix: 2.73 (0.27), residues: 384 sheet: 2.12 (0.65), residues: 60 loop : 0.42 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 490 TYR 0.008 0.001 TYR P 613 PHE 0.007 0.001 PHE B 111 TRP 0.006 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9670) covalent geometry : angle 0.71682 (13460) hydrogen bonds : bond 0.14134 ( 432) hydrogen bonds : angle 5.87688 ( 1154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LEU cc_start: 0.7214 (mp) cc_final: 0.6502 (mp) REVERT: B 98 MET cc_start: 0.7007 (mmm) cc_final: 0.6665 (mmt) REVERT: P 342 GLU cc_start: 0.7427 (pm20) cc_final: 0.7225 (pm20) REVERT: P 380 ASP cc_start: 0.6928 (t70) cc_final: 0.6655 (t70) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2789 time to fit residues: 71.8816 Evaluate side-chains 107 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 220 GLN P 284 ASN ** P 598 ASN ** 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 = 0.4097 r_free = 0.4097 target = 0.142664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114118 restraints weight = 46927.877| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.06 r_work: 0.3580 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9670 Z= 0.137 Angle : 0.576 5.165 13460 Z= 0.330 Chirality : 0.039 0.147 1498 Planarity : 0.004 0.045 1368 Dihedral : 22.731 174.507 2197 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 8.59 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.29), residues: 882 helix: 2.34 (0.27), residues: 387 sheet: 1.94 (0.61), residues: 58 loop : 0.31 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 412 TYR 0.011 0.001 TYR P 205 PHE 0.014 0.001 PHE B 111 TRP 0.006 0.001 TRP B 119 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9670) covalent geometry : angle 0.57648 (13460) hydrogen bonds : bond 0.05113 ( 432) hydrogen bonds : angle 4.88667 ( 1154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6320 (m-30) cc_final: 0.5837 (m-30) outliers start: 4 outliers final: 4 residues processed: 107 average time/residue: 0.1868 time to fit residues: 27.4616 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 308 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 0.0570 chunk 85 optimal weight: 6.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 284 ASN P 316 ASN ** P 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 817 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107282 restraints weight = 46550.280| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.94 r_work: 0.3491 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9670 Z= 0.200 Angle : 0.609 6.018 13460 Z= 0.347 Chirality : 0.043 0.199 1498 Planarity : 0.004 0.034 1368 Dihedral : 22.770 174.362 2197 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 8.59 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.29), residues: 882 helix: 1.94 (0.26), residues: 392 sheet: 0.97 (0.60), residues: 65 loop : 0.05 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 780 TYR 0.010 0.001 TYR B 5 PHE 0.013 0.002 PHE B 111 TRP 0.007 0.001 TRP P 724 HIS 0.003 0.001 HIS P 631 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9670) covalent geometry : angle 0.60949 (13460) hydrogen bonds : bond 0.05456 ( 432) hydrogen bonds : angle 4.72023 ( 1154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6398 (m-30) cc_final: 0.6126 (m-30) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.2042 time to fit residues: 27.9076 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 678 LEU Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 513 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.137235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108910 restraints weight = 47458.814| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.05 r_work: 0.3507 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9670 Z= 0.175 Angle : 0.583 6.403 13460 Z= 0.331 Chirality : 0.041 0.212 1498 Planarity : 0.004 0.036 1368 Dihedral : 22.794 174.979 2197 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.14 % Allowed : 10.23 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.28), residues: 882 helix: 1.89 (0.26), residues: 392 sheet: 0.72 (0.58), residues: 65 loop : -0.04 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 780 TYR 0.009 0.001 TYR P 205 PHE 0.013 0.001 PHE B 111 TRP 0.004 0.001 TRP P 724 HIS 0.003 0.001 HIS P 344 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9670) covalent geometry : angle 0.58260 (13460) hydrogen bonds : bond 0.05162 ( 432) hydrogen bonds : angle 4.57667 ( 1154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6054 (m-30) cc_final: 0.5848 (m-30) REVERT: P 158 PHE cc_start: 0.7629 (t80) cc_final: 0.7351 (t80) REVERT: P 186 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7992 (mmm-85) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.1728 time to fit residues: 23.3306 Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 183 ASN Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 677 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.0040 chunk 88 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106983 restraints weight = 47233.441| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.08 r_work: 0.3468 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9670 Z= 0.152 Angle : 0.557 6.054 13460 Z= 0.317 Chirality : 0.040 0.218 1498 Planarity : 0.004 0.033 1368 Dihedral : 22.794 176.494 2197 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.88 % Allowed : 10.48 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.28), residues: 882 helix: 1.95 (0.26), residues: 392 sheet: 0.49 (0.56), residues: 67 loop : -0.07 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 370 TYR 0.009 0.001 TYR P 205 PHE 0.009 0.001 PHE P 254 TRP 0.004 0.001 TRP P 724 HIS 0.003 0.001 HIS P 628 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9670) covalent geometry : angle 0.55715 (13460) hydrogen bonds : bond 0.05056 ( 432) hydrogen bonds : angle 4.41740 ( 1154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 GLU cc_start: 0.8183 (tp30) cc_final: 0.7821 (tp30) outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 0.1676 time to fit residues: 20.8185 Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 496 MET Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.135357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107789 restraints weight = 46187.420| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.90 r_work: 0.3493 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9670 Z= 0.138 Angle : 0.543 5.720 13460 Z= 0.309 Chirality : 0.040 0.192 1498 Planarity : 0.004 0.032 1368 Dihedral : 22.746 176.981 2197 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.76 % Allowed : 10.73 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.29), residues: 882 helix: 2.08 (0.26), residues: 391 sheet: 0.42 (0.56), residues: 67 loop : -0.07 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 520 TYR 0.008 0.001 TYR P 205 PHE 0.016 0.001 PHE P 158 TRP 0.003 0.001 TRP P 724 HIS 0.003 0.001 HIS P 671 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9670) covalent geometry : angle 0.54259 (13460) hydrogen bonds : bond 0.04970 ( 432) hydrogen bonds : angle 4.32604 ( 1154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.1983 time to fit residues: 23.9851 Evaluate side-chains 81 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 496 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105926 restraints weight = 47697.837| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.07 r_work: 0.3452 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9670 Z= 0.178 Angle : 0.568 6.159 13460 Z= 0.323 Chirality : 0.042 0.213 1498 Planarity : 0.004 0.032 1368 Dihedral : 22.739 177.822 2197 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.26 % Allowed : 10.98 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.28), residues: 882 helix: 1.97 (0.26), residues: 391 sheet: 0.25 (0.56), residues: 67 loop : -0.21 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 780 TYR 0.008 0.001 TYR B 5 PHE 0.023 0.001 PHE P 158 TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 628 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9670) covalent geometry : angle 0.56841 (13460) hydrogen bonds : bond 0.05195 ( 432) hydrogen bonds : angle 4.37069 ( 1154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.1945 time to fit residues: 24.2925 Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 294 LEU Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 496 MET Chi-restraints excluded: chain P residue 677 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.136134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.107709 restraints weight = 47583.021| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.09 r_work: 0.3476 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9670 Z= 0.132 Angle : 0.545 5.820 13460 Z= 0.308 Chirality : 0.040 0.231 1498 Planarity : 0.004 0.032 1368 Dihedral : 22.698 177.588 2197 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.14 % Allowed : 11.11 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.29), residues: 882 helix: 2.12 (0.26), residues: 391 sheet: 0.30 (0.57), residues: 67 loop : -0.19 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 818 TYR 0.011 0.001 TYR B 5 PHE 0.016 0.001 PHE P 158 TRP 0.004 0.001 TRP B 119 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9670) covalent geometry : angle 0.54484 (13460) hydrogen bonds : bond 0.04948 ( 432) hydrogen bonds : angle 4.25710 ( 1154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 467 ILE cc_start: 0.7522 (mt) cc_final: 0.7299 (mt) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.1924 time to fit residues: 24.2191 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 294 LEU Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 496 MET Chi-restraints excluded: chain P residue 677 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.132600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.104326 restraints weight = 48246.279| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.06 r_work: 0.3426 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9670 Z= 0.216 Angle : 0.616 6.797 13460 Z= 0.346 Chirality : 0.044 0.233 1498 Planarity : 0.004 0.031 1368 Dihedral : 22.805 178.735 2197 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.52 % Allowed : 11.11 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.28), residues: 882 helix: 1.72 (0.26), residues: 397 sheet: 0.18 (0.58), residues: 67 loop : -0.43 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 561 TYR 0.011 0.002 TYR B 5 PHE 0.013 0.002 PHE P 826 TRP 0.004 0.001 TRP P 724 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9670) covalent geometry : angle 0.61603 (13460) hydrogen bonds : bond 0.05549 ( 432) hydrogen bonds : angle 4.47786 ( 1154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 186 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7704 (mtt-85) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.1885 time to fit residues: 23.1393 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 294 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 496 MET Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.134925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106679 restraints weight = 47707.932| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.06 r_work: 0.3461 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9670 Z= 0.137 Angle : 0.555 5.732 13460 Z= 0.313 Chirality : 0.040 0.208 1498 Planarity : 0.003 0.031 1368 Dihedral : 22.742 178.008 2197 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.14 % Allowed : 11.99 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.28), residues: 882 helix: 1.97 (0.26), residues: 391 sheet: 0.20 (0.58), residues: 67 loop : -0.27 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 780 TYR 0.009 0.001 TYR P 205 PHE 0.009 0.001 PHE B 111 TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 631 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9670) covalent geometry : angle 0.55504 (13460) hydrogen bonds : bond 0.05076 ( 432) hydrogen bonds : angle 4.31238 ( 1154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 186 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7636 (mtt-85) REVERT: P 467 ILE cc_start: 0.7536 (mt) cc_final: 0.7329 (mt) REVERT: P 551 MET cc_start: 0.8036 (mmm) cc_final: 0.7652 (mmm) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.1849 time to fit residues: 22.0848 Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 294 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 496 MET Chi-restraints excluded: chain P residue 677 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.134407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.106097 restraints weight = 48090.614| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.07 r_work: 0.3453 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9670 Z= 0.159 Angle : 0.564 6.075 13460 Z= 0.318 Chirality : 0.041 0.203 1498 Planarity : 0.004 0.031 1368 Dihedral : 22.703 177.933 2197 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.26 % Allowed : 12.25 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.28), residues: 882 helix: 2.03 (0.26), residues: 385 sheet: 0.16 (0.58), residues: 67 loop : -0.32 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 780 TYR 0.008 0.001 TYR B 5 PHE 0.010 0.001 PHE B 111 TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9670) covalent geometry : angle 0.56357 (13460) hydrogen bonds : bond 0.05143 ( 432) hydrogen bonds : angle 4.32775 ( 1154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.82 seconds wall clock time: 74 minutes 53.24 seconds (4493.24 seconds total)