Starting phenix.real_space_refine on Sun Jun 15 14:03:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf3_45528/06_2025/9cf3_45528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf3_45528/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cf3_45528/06_2025/9cf3_45528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf3_45528/06_2025/9cf3_45528.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf3_45528/06_2025/9cf3_45528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf3_45528/06_2025/9cf3_45528.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.01, per 1000 atoms: 0.51 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: 4.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 8.74 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: 7.52 Time building geometry restraints manager: 5.59 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: 2.250 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: 0.330 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 47.830 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.540 ------------------------------------------------------------------------------- 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 : 5.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 PHE 0.007 0.001 PHE B 111 TYR 0.008 0.001 TYR P 613 ARG 0.002 0.000 ARG P 490 Details of bonding type rmsd hydrogen bonds : bond 0.14134 ( 432) hydrogen bonds : angle 5.87688 ( 1154) covalent geometry : bond 0.00237 ( 9670) covalent geometry : angle 0.71682 (13460) *********************** 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 : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LEU cc_start: 0.7214 (mp) cc_final: 0.6502 (mp) REVERT: B 98 MET cc_start: 0.7007 (mmm) cc_final: 0.6667 (mmt) REVERT: P 342 GLU cc_start: 0.7427 (pm20) cc_final: 0.7172 (pm20) REVERT: P 380 ASP cc_start: 0.6928 (t70) cc_final: 0.6657 (t70) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.6902 time to fit residues: 179.4864 Evaluate side-chains 108 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 513 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 = 0.4050 r_free = 0.4050 target = 0.138945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.109835 restraints weight = 46830.952| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.10 r_work: 0.3514 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9670 Z= 0.181 Angle : 0.606 5.606 13460 Z= 0.347 Chirality : 0.042 0.174 1498 Planarity : 0.005 0.050 1368 Dihedral : 22.762 173.332 2197 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.14 % Allowed : 8.46 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 882 helix: 2.20 (0.26), residues: 386 sheet: 1.30 (0.62), residues: 64 loop : 0.35 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 724 HIS 0.004 0.001 HIS B 90 PHE 0.012 0.001 PHE B 111 TYR 0.012 0.001 TYR P 205 ARG 0.004 0.001 ARG P 780 Details of bonding type rmsd hydrogen bonds : bond 0.05457 ( 432) hydrogen bonds : angle 4.94466 ( 1154) covalent geometry : bond 0.00398 ( 9670) covalent geometry : angle 0.60632 (13460) *********************** 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 107 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.217 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: B 7 ASP cc_start: 0.6164 (m-30) cc_final: 0.5709 (m-30) REVERT: B 60 LEU cc_start: 0.7127 (mp) cc_final: 0.6896 (mp) outliers start: 9 outliers final: 6 residues processed: 104 average time/residue: 0.4686 time to fit residues: 68.0111 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 : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 677 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 0.0070 chunk 79 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.137752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109879 restraints weight = 45563.039| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.92 r_work: 0.3530 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9670 Z= 0.141 Angle : 0.559 5.385 13460 Z= 0.319 Chirality : 0.039 0.180 1498 Planarity : 0.004 0.034 1368 Dihedral : 22.757 173.128 2197 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.63 % Allowed : 8.96 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.29), residues: 882 helix: 2.15 (0.26), residues: 387 sheet: 1.14 (0.60), residues: 65 loop : 0.18 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 724 HIS 0.003 0.001 HIS P 671 PHE 0.012 0.001 PHE B 81 TYR 0.010 0.001 TYR P 205 ARG 0.004 0.000 ARG P 412 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 432) hydrogen bonds : angle 4.66005 ( 1154) covalent geometry : bond 0.00306 ( 9670) covalent geometry : angle 0.55893 (13460) *********************** 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 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.417 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: 0.6359 (m-30) cc_final: 0.6064 (m-30) outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.4826 time to fit residues: 62.4683 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 117 CYS Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 308 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.136841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109205 restraints weight = 47019.128| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.13 r_work: 0.3492 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9670 Z= 0.193 Angle : 0.603 6.047 13460 Z= 0.343 Chirality : 0.042 0.192 1498 Planarity : 0.004 0.036 1368 Dihedral : 22.855 174.965 2197 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.52 % Allowed : 8.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 882 helix: 1.93 (0.26), residues: 386 sheet: 0.77 (0.59), residues: 65 loop : -0.02 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 724 HIS 0.004 0.001 HIS B 89 PHE 0.022 0.002 PHE P 158 TYR 0.010 0.001 TYR P 205 ARG 0.003 0.000 ARG P 780 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 432) hydrogen bonds : angle 4.61481 ( 1154) covalent geometry : bond 0.00432 ( 9670) covalent geometry : angle 0.60339 (13460) *********************** 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 98 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 2.050 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: B 7 ASP cc_start: 0.6136 (m-30) cc_final: 0.5909 (m-30) REVERT: B 153 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7701 (mmt-90) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.6032 time to fit residues: 83.2437 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 : 1.360 ------------------------------------------------------------------------------- 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 112 THR Chi-restraints excluded: chain P residue 183 ASN Chi-restraints excluded: chain P residue 308 ASP Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 85 optimal weight: 0.0070 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.139350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.111160 restraints weight = 47601.720| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.04 r_work: 0.3540 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3983 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= 0.127 Angle : 0.545 5.240 13460 Z= 0.309 Chirality : 0.039 0.198 1498 Planarity : 0.004 0.034 1368 Dihedral : 22.842 175.533 2197 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.76 % Allowed : 9.60 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 882 helix: 2.16 (0.26), residues: 386 sheet: 0.77 (0.58), residues: 65 loop : 0.08 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 724 HIS 0.003 0.001 HIS P 671 PHE 0.016 0.001 PHE P 158 TYR 0.009 0.001 TYR P 205 ARG 0.002 0.000 ARG P 490 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 432) hydrogen bonds : angle 4.40291 ( 1154) covalent geometry : bond 0.00277 ( 9670) covalent geometry : angle 0.54522 (13460) *********************** 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: 6 poor density : 84 time to evaluate : 1.412 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: 0.5936 (m-30) cc_final: 0.5719 (m-30) REVERT: B 32 GLU cc_start: 0.8260 (tp30) cc_final: 0.7928 (tp30) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.4570 time to fit residues: 57.0210 Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 327 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.134246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105435 restraints weight = 47576.981| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.09 r_work: 0.3444 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9670 Z= 0.200 Angle : 0.592 6.305 13460 Z= 0.335 Chirality : 0.042 0.215 1498 Planarity : 0.004 0.033 1368 Dihedral : 22.923 177.373 2197 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.14 % Allowed : 9.72 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 882 helix: 2.00 (0.26), residues: 385 sheet: 0.36 (0.57), residues: 65 loop : -0.04 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 724 HIS 0.004 0.001 HIS P 628 PHE 0.011 0.001 PHE B 111 TYR 0.010 0.001 TYR B 5 ARG 0.003 0.000 ARG P 780 Details of bonding type rmsd hydrogen bonds : bond 0.05364 ( 432) hydrogen bonds : angle 4.49471 ( 1154) covalent geometry : bond 0.00446 ( 9670) covalent geometry : angle 0.59222 (13460) *********************** 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 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.354 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 32 GLU cc_start: 0.8182 (tp30) cc_final: 0.7826 (tp30) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.4882 time to fit residues: 62.2862 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 : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 327 THR Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.108421 restraints weight = 46329.892| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.86 r_work: 0.3485 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9670 Z= 0.150 Angle : 0.556 5.566 13460 Z= 0.314 Chirality : 0.040 0.237 1498 Planarity : 0.004 0.033 1368 Dihedral : 22.839 177.783 2197 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.52 % Allowed : 9.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 882 helix: 2.10 (0.26), residues: 385 sheet: 0.31 (0.58), residues: 65 loop : -0.04 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 724 HIS 0.003 0.001 HIS P 671 PHE 0.012 0.001 PHE P 158 TYR 0.009 0.001 TYR P 205 ARG 0.003 0.000 ARG P 186 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 432) hydrogen bonds : angle 4.37593 ( 1154) covalent geometry : bond 0.00330 ( 9670) covalent geometry : angle 0.55641 (13460) *********************** 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 97 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.367 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 outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.4683 time to fit residues: 60.7155 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 112 THR Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 613 TYR Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 0.0970 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106624 restraints weight = 47497.700| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.08 r_work: 0.3465 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4523 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= 0.155 Angle : 0.557 5.812 13460 Z= 0.315 Chirality : 0.041 0.221 1498 Planarity : 0.004 0.033 1368 Dihedral : 22.705 177.775 2197 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.64 % Allowed : 10.23 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.28), residues: 882 helix: 2.07 (0.26), residues: 385 sheet: 0.18 (0.57), residues: 67 loop : -0.14 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 671 PHE 0.040 0.001 PHE P 158 TYR 0.008 0.001 TYR P 205 ARG 0.003 0.000 ARG P 818 Details of bonding type rmsd hydrogen bonds : bond 0.05091 ( 432) hydrogen bonds : angle 4.35325 ( 1154) covalent geometry : bond 0.00341 ( 9670) covalent geometry : angle 0.55670 (13460) *********************** 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 95 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.366 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 outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.4467 time to fit residues: 58.7649 Evaluate side-chains 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 49 SER 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 294 LEU Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 677 SER Chi-restraints excluded: chain P residue 699 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.132397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104066 restraints weight = 48236.798| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.10 r_work: 0.3420 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9670 Z= 0.235 Angle : 0.626 6.635 13460 Z= 0.352 Chirality : 0.044 0.220 1498 Planarity : 0.004 0.031 1368 Dihedral : 22.798 178.996 2197 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.89 % Allowed : 10.48 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.28), residues: 882 helix: 1.68 (0.26), residues: 391 sheet: 0.08 (0.59), residues: 65 loop : -0.40 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 724 HIS 0.005 0.001 HIS B 89 PHE 0.013 0.002 PHE P 826 TYR 0.014 0.002 TYR B 5 ARG 0.004 0.001 ARG P 561 Details of bonding type rmsd hydrogen bonds : bond 0.05607 ( 432) hydrogen bonds : angle 4.53710 ( 1154) covalent geometry : bond 0.00527 ( 9670) covalent geometry : angle 0.62598 (13460) *********************** 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 97 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 186 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7945 (mtt-85) REVERT: P 655 ILE cc_start: 0.9129 (mt) cc_final: 0.8866 (tp) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.4608 time to fit residues: 60.9015 Evaluate side-chains 91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 49 SER 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 294 LEU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 327 THR Chi-restraints excluded: chain P residue 433 ASP Chi-restraints excluded: chain P residue 503 ASP 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 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 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 = 0.3992 r_free = 0.3992 target = 0.134801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106492 restraints weight = 47660.508| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.07 r_work: 0.3460 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9670 Z= 0.141 Angle : 0.564 6.242 13460 Z= 0.317 Chirality : 0.040 0.201 1498 Planarity : 0.004 0.032 1368 Dihedral : 22.709 178.017 2197 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.14 % Allowed : 11.36 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 882 helix: 2.02 (0.26), residues: 384 sheet: 0.10 (0.59), residues: 67 loop : -0.24 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 724 HIS 0.004 0.001 HIS P 631 PHE 0.014 0.001 PHE P 158 TYR 0.009 0.001 TYR P 205 ARG 0.003 0.000 ARG P 520 Details of bonding type rmsd hydrogen bonds : bond 0.05113 ( 432) hydrogen bonds : angle 4.34125 ( 1154) covalent geometry : bond 0.00308 ( 9670) covalent geometry : angle 0.56394 (13460) ********************** 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 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 655 ILE cc_start: 0.9100 (mt) cc_final: 0.8843 (tp) outliers start: 9 outliers final: 8 residues processed: 85 average time/residue: 0.5433 time to fit residues: 66.2009 Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.134955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106712 restraints weight = 47724.725| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.06 r_work: 0.3466 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9670 Z= 0.145 Angle : 0.556 5.739 13460 Z= 0.314 Chirality : 0.040 0.193 1498 Planarity : 0.004 0.032 1368 Dihedral : 22.641 177.594 2197 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.39 % Allowed : 11.49 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 882 helix: 2.12 (0.26), residues: 384 sheet: 0.09 (0.59), residues: 67 loop : -0.24 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 724 HIS 0.004 0.001 HIS P 671 PHE 0.011 0.001 PHE P 158 TYR 0.009 0.001 TYR P 205 ARG 0.003 0.000 ARG P 520 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 432) hydrogen bonds : angle 4.31606 ( 1154) covalent geometry : bond 0.00319 ( 9670) covalent geometry : angle 0.55611 (13460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10706.92 seconds wall clock time: 188 minutes 18.81 seconds (11298.81 seconds total)