Starting phenix.real_space_refine on Mon Jun 16 03:37:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf2_45527/06_2025/9cf2_45527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf2_45527/06_2025/9cf2_45527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cf2_45527/06_2025/9cf2_45527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf2_45527/06_2025/9cf2_45527.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf2_45527/06_2025/9cf2_45527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf2_45527/06_2025/9cf2_45527.cif" } resolution = 3.15 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= 0.002 sd= 0.030 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 121 5.49 5 S 35 5.16 5 C 5804 2.51 5 N 1707 2.21 5 O 2071 1.98 5 H 8649 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: 18387 Number of models: 1 Model: "" Number of chains: 7 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: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Classifications: {'DNA': 11} 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: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 830 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} 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': 4, 'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 7, 'rna3p': 48} Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 449 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 449 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Time building chain proxies: 8.82, per 1000 atoms: 0.48 Number of scatterers: 18387 At special positions: 0 Unit cell: (80.025, 120.45, 122.925, 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 121 15.00 O 2071 8.00 N 1707 7.00 C 5804 6.00 H 8649 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: 5.02 Conformation dependent library (CDL) restraints added in 1.2 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: 38 helices and 7 sheets defined 51.6% alpha, 11.3% beta 48 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 9.40 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: 3.677A 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 122 Processing helix chain 'P' and resid 123 through 155 Processing helix chain 'P' and resid 159 through 164 removed outlier: 3.851A pdb=" N LEU P 163 " --> pdb=" O ALA P 159 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE P 164 " --> pdb=" O PHE P 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 159 through 164' Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.614A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 Processing helix chain 'P' and resid 188 through 210 removed outlier: 3.801A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 255 removed outlier: 3.756A pdb=" N ALA P 228 " --> pdb=" O LEU P 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 5.115A 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 removed outlier: 3.547A pdb=" N ALA P 269 " --> pdb=" O LYS P 265 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN P 270 " --> pdb=" O GLU P 266 " (cutoff:3.500A) 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 328 through 331 Processing helix chain 'P' and resid 332 through 340 removed outlier: 4.203A 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 380 through 388 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: 3.602A pdb=" N TRP P 404 " --> pdb=" O LYS P 400 " (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 530 removed outlier: 5.274A pdb=" N CYS P 518 " --> pdb=" O ASP P 514 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER P 519 " --> pdb=" O ARG P 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 542 Processing helix chain 'P' and resid 550 through 573 removed outlier: 4.959A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 623 through 639 removed outlier: 3.838A pdb=" N SER P 627 " --> pdb=" O ILE P 623 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN P 639 " --> pdb=" O GLN P 635 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 removed outlier: 3.964A pdb=" N GLU P 645 " --> pdb=" O LYS P 641 " (cutoff:3.500A) Processing helix chain 'P' and resid 648 through 665 removed outlier: 3.761A pdb=" N GLU P 664 " --> pdb=" O LYS P 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 669 through 679 Processing helix chain 'P' and resid 680 through 684 Processing helix chain 'P' and resid 686 through 713 Processing helix chain 'P' and resid 736 through 747 Processing helix chain 'P' and resid 780 through 784 Processing helix chain 'P' and resid 818 through 837 Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.649A pdb=" N ARG B 53 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 95 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET B 98 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 126 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 16 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.610A 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: 5.132A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLN P 442 " --> pdb=" O GLN P 427 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN P 427 " --> pdb=" O GLN P 442 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU P 430 " --> pdb=" O VAL P 379 " (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: 6.244A pdb=" N VAL P 483 " --> pdb=" O VAL P 720 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLY P 722 " --> pdb=" O VAL P 483 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N MET P 485 " --> pdb=" O GLY P 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 592 through 593 Processing sheet with id=AA6, first strand: chain 'P' and resid 770 through 771 Processing sheet with id=AA7, first strand: chain 'P' and resid 775 through 777 350 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 6.08 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: 8632 1.03 - 1.23: 83 1.23 - 1.42: 4392 1.42 - 1.62: 5685 1.62 - 1.81: 53 Bond restraints: 18845 Sorted by residual: bond pdb=" C1' A W 29 " pdb=" N9 A W 29 " ideal model delta sigma weight residual 1.475 1.493 -0.018 1.50e-02 4.44e+03 1.47e+00 bond pdb=" C3' A W 28 " pdb=" O3' A W 28 " ideal model delta sigma weight residual 1.417 1.434 -0.017 1.50e-02 4.44e+03 1.35e+00 bond pdb=" O5' A W 33 " pdb=" C5' A W 33 " ideal model delta sigma weight residual 1.420 1.436 -0.016 1.50e-02 4.44e+03 1.13e+00 bond pdb=" C3' DT T 1 " pdb=" C2' DT T 1 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 9.14e-01 bond pdb=" C ILE P 373 " pdb=" N PRO P 374 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.30e-02 5.92e+03 8.83e-01 ... (remaining 18840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 33906 2.56 - 5.13: 168 5.13 - 7.69: 2 7.69 - 10.26: 8 10.26 - 12.82: 4 Bond angle restraints: 34088 Sorted by residual: angle pdb=" N ILE P 580 " pdb=" CA ILE P 580 " pdb=" C ILE P 580 " ideal model delta sigma weight residual 113.71 109.43 4.28 9.50e-01 1.11e+00 2.03e+01 angle pdb=" OP1 A W 29 " pdb=" P A W 29 " pdb=" OP2 A W 29 " ideal model delta sigma weight residual 119.60 106.78 12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" P A W 33 " pdb=" O5' A W 33 " pdb=" C5' A W 33 " ideal model delta sigma weight residual 120.90 127.10 -6.20 1.50e+00 4.44e-01 1.71e+01 angle pdb=" O3' A W 28 " pdb=" P A W 29 " pdb=" OP1 A W 29 " ideal model delta sigma weight residual 108.00 119.67 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" OP1 A W 32 " pdb=" P A W 32 " pdb=" OP2 A W 32 " ideal model delta sigma weight residual 119.60 108.64 10.96 3.00e+00 1.11e-01 1.33e+01 ... (remaining 34083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 8121 35.18 - 70.36: 458 70.36 - 105.54: 27 105.54 - 140.72: 7 140.72 - 175.90: 4 Dihedral angle restraints: 8617 sinusoidal: 5491 harmonic: 3126 Sorted by residual: dihedral pdb=" O4' U W 15 " pdb=" C1' U W 15 " pdb=" N1 U W 15 " pdb=" C2 U W 15 " ideal model delta sinusoidal sigma weight residual -128.00 39.23 -167.23 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" O4' U W 17 " pdb=" C1' U W 17 " pdb=" N1 U W 17 " pdb=" C2 U W 17 " ideal model delta sinusoidal sigma weight residual -128.00 27.16 -155.16 1 1.70e+01 3.46e-03 6.34e+01 dihedral pdb=" CA TYR P 600 " pdb=" C TYR P 600 " pdb=" N TYR P 601 " pdb=" CA TYR P 601 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1511 0.083 - 0.165: 71 0.165 - 0.248: 3 0.248 - 0.331: 2 0.331 - 0.413: 3 Chirality restraints: 1590 Sorted by residual: chirality pdb=" P DT T -1 " pdb=" OP1 DT T -1 " pdb=" OP2 DT T -1 " pdb=" O5' DT T -1 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" P A W 29 " pdb=" OP1 A W 29 " pdb=" OP2 A W 29 " pdb=" O5' A W 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" P DT T 0 " pdb=" OP1 DT T 0 " pdb=" OP2 DT T 0 " pdb=" O5' DT T 0 " both_signs ideal model delta sigma weight residual True 2.35 -2.69 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 1587 not shown) Planarity restraints: 2323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C W 36 " 0.017 2.00e-02 2.50e+03 7.81e-03 1.68e+00 pdb=" N1 C W 36 " -0.018 2.00e-02 2.50e+03 pdb=" C2 C W 36 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C W 36 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C W 36 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C W 36 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C W 36 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C W 36 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C W 36 " -0.003 2.00e-02 2.50e+03 pdb=" H5 C W 36 " 0.002 2.00e-02 2.50e+03 pdb=" H6 C W 36 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN P 287 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO P 288 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO P 288 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 288 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN P 530 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO P 531 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO P 531 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO P 531 " -0.017 5.00e-02 4.00e+02 ... (remaining 2320 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 279 2.07 - 2.70: 27517 2.70 - 3.34: 51405 3.34 - 3.97: 65593 3.97 - 4.60: 104126 Nonbonded interactions: 248920 Sorted by model distance: nonbonded pdb=" OH TYR P 225 " pdb=" OD2 ASP P 380 " model vdw 1.441 2.800 nonbonded pdb="HO2' U W 31 " pdb=" OP2 A W 32 " model vdw 1.562 2.450 nonbonded pdb=" O THR P 759 " pdb="HD21 ASN P 825 " model vdw 1.568 2.450 nonbonded pdb="HO2' A W 29 " pdb=" O5' U W 30 " model vdw 1.592 2.450 nonbonded pdb="HH22 ARG P 818 " pdb=" OP2 DT Y 13 " model vdw 1.618 2.450 ... (remaining 248915 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: 2.230 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: 0.280 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 49.010 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 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 0.028 10196 Z= 0.126 Angle : 0.615 12.824 14269 Z= 0.345 Chirality : 0.042 0.413 1590 Planarity : 0.003 0.032 1391 Dihedral : 18.512 175.903 4334 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 2.60 (0.30), residues: 882 helix: 3.23 (0.28), residues: 364 sheet: 1.10 (0.60), residues: 79 loop : 0.62 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP P 816 HIS 0.001 0.000 HIS P 642 PHE 0.008 0.001 PHE P 158 TYR 0.006 0.001 TYR P 141 ARG 0.001 0.000 ARG P 282 Details of bonding type rmsd hydrogen bonds : bond 0.15325 ( 464) hydrogen bonds : angle 5.82944 ( 1220) covalent geometry : bond 0.00245 (10196) covalent geometry : angle 0.61491 (14269) *********************** 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 279 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 VAL cc_start: 0.7288 (t) cc_final: 0.6882 (t) REVERT: B 106 ASN cc_start: 0.7067 (m-40) cc_final: 0.6712 (m-40) REVERT: P 112 THR cc_start: 0.7345 (t) cc_final: 0.7084 (p) REVERT: P 160 PHE cc_start: 0.7614 (t80) cc_final: 0.7354 (t80) REVERT: P 171 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6326 (mm-30) REVERT: P 195 ARG cc_start: 0.6956 (ttm170) cc_final: 0.6687 (ttm-80) REVERT: P 202 LYS cc_start: 0.7587 (tttt) cc_final: 0.7273 (ttpp) REVERT: P 205 TYR cc_start: 0.7738 (t80) cc_final: 0.7338 (t80) REVERT: P 212 THR cc_start: 0.7622 (m) cc_final: 0.7313 (p) REVERT: P 254 PHE cc_start: 0.7554 (t80) cc_final: 0.7343 (t80) REVERT: P 310 LYS cc_start: 0.8223 (tttt) cc_final: 0.8000 (ttpp) REVERT: P 395 LEU cc_start: 0.8320 (tp) cc_final: 0.8104 (tt) REVERT: P 422 LYS cc_start: 0.7939 (mttt) cc_final: 0.7700 (mttp) REVERT: P 484 LEU cc_start: 0.7091 (mt) cc_final: 0.6859 (mp) REVERT: P 503 ASP cc_start: 0.7082 (p0) cc_final: 0.6627 (p0) REVERT: P 504 LYS cc_start: 0.7742 (tttt) cc_final: 0.7405 (ttpp) REVERT: P 540 TYR cc_start: 0.7535 (t80) cc_final: 0.7212 (t80) REVERT: P 556 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6940 (mt-10) REVERT: P 584 TYR cc_start: 0.8378 (m-80) cc_final: 0.8155 (m-80) REVERT: P 656 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7454 (mt-10) REVERT: P 672 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8083 (mtpt) REVERT: P 699 ASP cc_start: 0.6625 (m-30) cc_final: 0.6381 (m-30) REVERT: P 752 TYR cc_start: 0.7933 (m-80) cc_final: 0.7708 (m-80) REVERT: P 769 ASP cc_start: 0.7161 (p0) cc_final: 0.6801 (p0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.7413 time to fit residues: 262.3039 Evaluate side-chains 233 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 300 ASN P 353 GLN P 701 ASN P 817 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127491 restraints weight = 36847.867| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.72 r_work: 0.3514 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10196 Z= 0.218 Angle : 0.598 6.728 14269 Z= 0.346 Chirality : 0.044 0.197 1590 Planarity : 0.004 0.040 1391 Dihedral : 22.949 172.553 2476 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.15 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 (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: 2.03 (0.28), residues: 882 helix: 2.59 (0.26), residues: 368 sheet: 0.51 (0.55), residues: 91 loop : 0.51 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 724 HIS 0.003 0.001 HIS P 631 PHE 0.019 0.002 PHE B 111 TYR 0.014 0.002 TYR P 141 ARG 0.005 0.001 ARG P 703 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 464) hydrogen bonds : angle 4.66985 ( 1220) covalent geometry : bond 0.00477 (10196) covalent geometry : angle 0.59828 (14269) *********************** 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 238 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 234 time to evaluate : 1.137 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: B 27 VAL cc_start: 0.7328 (t) cc_final: 0.7082 (t) REVERT: B 106 ASN cc_start: 0.7866 (m-40) cc_final: 0.7509 (m-40) REVERT: P 160 PHE cc_start: 0.7906 (t80) cc_final: 0.7560 (t80) REVERT: P 202 LYS cc_start: 0.8291 (tttt) cc_final: 0.7984 (ttpp) REVERT: P 212 THR cc_start: 0.8226 (m) cc_final: 0.7922 (p) REVERT: P 380 ASP cc_start: 0.6884 (t0) cc_final: 0.6629 (t0) REVERT: P 395 LEU cc_start: 0.8464 (tp) cc_final: 0.8224 (tt) REVERT: P 399 GLU cc_start: 0.7642 (mm-30) cc_final: 0.6993 (mm-30) REVERT: P 422 LYS cc_start: 0.8448 (mttt) cc_final: 0.8202 (mttt) REVERT: P 504 LYS cc_start: 0.8307 (tttt) cc_final: 0.8033 (ttmm) REVERT: P 529 LEU cc_start: 0.8186 (mt) cc_final: 0.7915 (mp) REVERT: P 536 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7538 (mm-30) REVERT: P 565 LYS cc_start: 0.8458 (pttt) cc_final: 0.8137 (pttm) REVERT: P 584 TYR cc_start: 0.8696 (m-80) cc_final: 0.8414 (m-80) REVERT: P 637 MET cc_start: 0.8835 (ttt) cc_final: 0.8577 (ttm) REVERT: P 653 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7335 (mtp180) REVERT: P 656 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7673 (mt-10) REVERT: P 672 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8408 (mtpt) REVERT: P 695 LYS cc_start: 0.8028 (tppt) cc_final: 0.7408 (tptm) REVERT: P 699 ASP cc_start: 0.7885 (m-30) cc_final: 0.7612 (m-30) REVERT: P 784 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7442 (tm-30) REVERT: P 787 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7502 (mm-40) REVERT: P 819 ASP cc_start: 0.7675 (m-30) cc_final: 0.7353 (m-30) REVERT: P 835 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7263 (mt-10) outliers start: 4 outliers final: 2 residues processed: 235 average time/residue: 0.6622 time to fit residues: 198.4293 Evaluate side-chains 218 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 476 LYS Chi-restraints excluded: chain P residue 643 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS P 513 ASN P 701 ASN P 817 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.150855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125306 restraints weight = 36780.193| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.72 r_work: 0.3480 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10196 Z= 0.193 Angle : 0.576 4.837 14269 Z= 0.333 Chirality : 0.042 0.156 1590 Planarity : 0.004 0.039 1391 Dihedral : 22.983 175.141 2476 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.26 % Allowed : 9.72 % Favored : 89.02 % 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: 1.72 (0.28), residues: 882 helix: 2.29 (0.26), residues: 377 sheet: 0.29 (0.53), residues: 91 loop : 0.35 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 PHE 0.013 0.001 PHE B 110 TYR 0.015 0.001 TYR P 205 ARG 0.009 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 464) hydrogen bonds : angle 4.45907 ( 1220) covalent geometry : bond 0.00422 (10196) covalent geometry : angle 0.57560 (14269) *********************** 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 232 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 222 time to evaluate : 1.264 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 106 ASN cc_start: 0.7973 (m-40) cc_final: 0.7685 (m-40) REVERT: P 114 ILE cc_start: 0.8385 (mm) cc_final: 0.8180 (tt) REVERT: P 202 LYS cc_start: 0.8305 (tttt) cc_final: 0.8017 (ttpp) REVERT: P 212 THR cc_start: 0.8235 (m) cc_final: 0.7902 (p) REVERT: P 255 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8106 (mmtp) REVERT: P 380 ASP cc_start: 0.6849 (t0) cc_final: 0.6600 (t0) REVERT: P 395 LEU cc_start: 0.8521 (tp) cc_final: 0.8261 (tt) REVERT: P 399 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6865 (mm-30) REVERT: P 422 LYS cc_start: 0.8410 (mttt) cc_final: 0.8140 (mttp) REVERT: P 504 LYS cc_start: 0.8380 (tttt) cc_final: 0.8089 (ttmm) REVERT: P 529 LEU cc_start: 0.8198 (mt) cc_final: 0.7909 (mp) REVERT: P 536 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7607 (mm-30) REVERT: P 565 LYS cc_start: 0.8462 (pttt) cc_final: 0.8196 (pttm) REVERT: P 582 GLU cc_start: 0.7726 (tp30) cc_final: 0.7329 (tm-30) REVERT: P 637 MET cc_start: 0.8790 (ttt) cc_final: 0.8508 (ttm) REVERT: P 653 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7409 (mtp180) REVERT: P 656 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7773 (mt-10) REVERT: P 660 LYS cc_start: 0.8860 (tttt) cc_final: 0.8628 (tttt) REVERT: P 672 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8421 (mtpt) REVERT: P 695 LYS cc_start: 0.7991 (tppt) cc_final: 0.7400 (tptm) REVERT: P 699 ASP cc_start: 0.7960 (m-30) cc_final: 0.7698 (m-30) REVERT: P 787 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7568 (mm-40) REVERT: P 819 ASP cc_start: 0.7791 (m-30) cc_final: 0.7483 (m-30) outliers start: 10 outliers final: 6 residues processed: 224 average time/residue: 0.6527 time to fit residues: 187.5639 Evaluate side-chains 219 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 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 89 HIS B 109 GLN P 385 ASN P 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120127 restraints weight = 36952.114| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.82 r_work: 0.3397 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10196 Z= 0.361 Angle : 0.671 5.262 14269 Z= 0.383 Chirality : 0.051 0.197 1590 Planarity : 0.005 0.054 1391 Dihedral : 23.343 176.287 2476 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.52 % Allowed : 10.86 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.08 (0.27), residues: 882 helix: 1.74 (0.25), residues: 381 sheet: -0.11 (0.51), residues: 91 loop : 0.02 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 816 HIS 0.007 0.002 HIS P 201 PHE 0.017 0.002 PHE P 235 TYR 0.020 0.002 TYR P 141 ARG 0.007 0.001 ARG P 818 Details of bonding type rmsd hydrogen bonds : bond 0.05740 ( 464) hydrogen bonds : angle 4.57967 ( 1220) covalent geometry : bond 0.00797 (10196) covalent geometry : angle 0.67066 (14269) *********************** 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 240 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 1.349 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: P 202 LYS cc_start: 0.8380 (tttt) cc_final: 0.8089 (ttpp) REVERT: P 212 THR cc_start: 0.8242 (m) cc_final: 0.7909 (p) REVERT: P 255 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8124 (mmtp) REVERT: P 304 SER cc_start: 0.8867 (m) cc_final: 0.8639 (t) REVERT: P 380 ASP cc_start: 0.7065 (t0) cc_final: 0.6766 (t0) REVERT: P 395 LEU cc_start: 0.8620 (tp) cc_final: 0.8358 (tt) REVERT: P 399 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6983 (mm-30) REVERT: P 422 LYS cc_start: 0.8516 (mttt) cc_final: 0.8225 (mttm) REVERT: P 504 LYS cc_start: 0.8433 (tttt) cc_final: 0.8173 (ttpt) REVERT: P 536 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7600 (mm-30) REVERT: P 540 TYR cc_start: 0.8201 (t80) cc_final: 0.7849 (t80) REVERT: P 565 LYS cc_start: 0.8507 (pttt) cc_final: 0.8231 (pttm) REVERT: P 604 LEU cc_start: 0.8348 (tt) cc_final: 0.8034 (tp) REVERT: P 636 ILE cc_start: 0.8626 (mt) cc_final: 0.8415 (tt) REVERT: P 653 ARG cc_start: 0.7754 (mtt180) cc_final: 0.7525 (mtp180) REVERT: P 660 LYS cc_start: 0.8885 (tttt) cc_final: 0.8646 (tttt) REVERT: P 672 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8498 (mtpt) REVERT: P 695 LYS cc_start: 0.8088 (tppt) cc_final: 0.7557 (tptm) REVERT: P 699 ASP cc_start: 0.8017 (m-30) cc_final: 0.7774 (m-30) REVERT: P 701 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7612 (t0) REVERT: P 787 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7714 (mm-40) REVERT: P 819 ASP cc_start: 0.8015 (m-30) cc_final: 0.7710 (m-30) REVERT: P 835 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7284 (mt-10) outliers start: 12 outliers final: 9 residues processed: 232 average time/residue: 0.7052 time to fit residues: 207.8124 Evaluate side-chains 229 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 385 ASN Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 701 ASN Chi-restraints excluded: chain P residue 729 THR Chi-restraints excluded: chain P residue 836 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN P 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123618 restraints weight = 36611.156| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.64 r_work: 0.3468 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10196 Z= 0.181 Angle : 0.586 4.453 14269 Z= 0.337 Chirality : 0.042 0.149 1590 Planarity : 0.004 0.054 1391 Dihedral : 23.228 174.387 2476 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.14 % Allowed : 11.87 % Favored : 86.99 % 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 (0.27), residues: 882 helix: 1.84 (0.25), residues: 381 sheet: -0.08 (0.52), residues: 86 loop : 0.01 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 PHE 0.019 0.001 PHE B 110 TYR 0.023 0.001 TYR P 386 ARG 0.004 0.000 ARG P 282 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 464) hydrogen bonds : angle 4.39301 ( 1220) covalent geometry : bond 0.00396 (10196) covalent geometry : angle 0.58595 (14269) *********************** 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 227 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 1.200 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 27 VAL cc_start: 0.7687 (t) cc_final: 0.7413 (t) REVERT: P 202 LYS cc_start: 0.8370 (tttt) cc_final: 0.8106 (ttpp) REVERT: P 212 THR cc_start: 0.8286 (m) cc_final: 0.8011 (p) REVERT: P 255 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8194 (mmtp) REVERT: P 380 ASP cc_start: 0.6938 (t0) cc_final: 0.6721 (t0) REVERT: P 399 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6888 (mm-30) REVERT: P 422 LYS cc_start: 0.8485 (mttt) cc_final: 0.8234 (mttm) REVERT: P 504 LYS cc_start: 0.8474 (tttt) cc_final: 0.8220 (ttpt) REVERT: P 536 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7570 (mm-30) REVERT: P 565 LYS cc_start: 0.8473 (pttt) cc_final: 0.8238 (pttm) REVERT: P 653 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7522 (mtp180) REVERT: P 660 LYS cc_start: 0.8846 (tttt) cc_final: 0.8629 (tttt) REVERT: P 672 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8468 (mtpt) REVERT: P 695 LYS cc_start: 0.8066 (tppt) cc_final: 0.7555 (tptm) REVERT: P 699 ASP cc_start: 0.7954 (m-30) cc_final: 0.7706 (m-30) REVERT: P 819 ASP cc_start: 0.7945 (m-30) cc_final: 0.7570 (m-30) REVERT: P 835 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7148 (mt-10) outliers start: 9 outliers final: 7 residues processed: 220 average time/residue: 0.7194 time to fit residues: 199.6312 Evaluate side-chains 221 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 729 THR Chi-restraints excluded: chain P residue 836 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119464 restraints weight = 36675.243| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.71 r_work: 0.3405 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 10196 Z= 0.401 Angle : 0.698 5.962 14269 Z= 0.395 Chirality : 0.053 0.214 1590 Planarity : 0.005 0.044 1391 Dihedral : 23.449 177.289 2476 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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 : 0.12 % 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: 0.68 (0.27), residues: 882 helix: 1.40 (0.25), residues: 381 sheet: -0.24 (0.51), residues: 86 loop : -0.20 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 816 HIS 0.007 0.002 HIS P 201 PHE 0.020 0.002 PHE B 110 TYR 0.022 0.002 TYR P 141 ARG 0.005 0.001 ARG P 688 Details of bonding type rmsd hydrogen bonds : bond 0.06007 ( 464) hydrogen bonds : angle 4.62768 ( 1220) covalent geometry : bond 0.00892 (10196) covalent geometry : angle 0.69806 (14269) *********************** 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 231 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 1.176 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 27 VAL cc_start: 0.7808 (t) cc_final: 0.7533 (t) REVERT: B 81 PHE cc_start: 0.7730 (p90) cc_final: 0.7400 (p90) REVERT: P 106 ARG cc_start: 0.7083 (ttt-90) cc_final: 0.6854 (ttt-90) REVERT: P 195 ARG cc_start: 0.7968 (ttm170) cc_final: 0.5137 (ttm170) REVERT: P 202 LYS cc_start: 0.8424 (tttt) cc_final: 0.8133 (ttpp) REVERT: P 212 THR cc_start: 0.8287 (m) cc_final: 0.7934 (p) REVERT: P 255 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8206 (mmtp) REVERT: P 342 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7979 (pm20) REVERT: P 380 ASP cc_start: 0.7012 (t0) cc_final: 0.6715 (t0) REVERT: P 393 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8037 (mttm) REVERT: P 399 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7002 (mm-30) REVERT: P 422 LYS cc_start: 0.8511 (mttt) cc_final: 0.8259 (mttm) REVERT: P 504 LYS cc_start: 0.8481 (tttt) cc_final: 0.8218 (ttpt) REVERT: P 514 ASP cc_start: 0.8287 (t70) cc_final: 0.7964 (t0) REVERT: P 536 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7625 (mm-30) REVERT: P 565 LYS cc_start: 0.8490 (pttt) cc_final: 0.8260 (pttm) REVERT: P 582 GLU cc_start: 0.7776 (tp30) cc_final: 0.7494 (tm-30) REVERT: P 604 LEU cc_start: 0.8462 (tt) cc_final: 0.8175 (tp) REVERT: P 653 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7608 (mtp180) REVERT: P 660 LYS cc_start: 0.8899 (tttt) cc_final: 0.8676 (tttt) REVERT: P 672 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8495 (mtpt) REVERT: P 695 LYS cc_start: 0.8148 (tppt) cc_final: 0.7632 (tptm) REVERT: P 699 ASP cc_start: 0.7974 (m-30) cc_final: 0.7735 (m-30) REVERT: P 819 ASP cc_start: 0.8057 (m-30) cc_final: 0.7719 (m-30) REVERT: P 835 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 11 outliers final: 8 residues processed: 227 average time/residue: 0.7161 time to fit residues: 204.7102 Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 342 GLU Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 396 LYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 701 ASN Chi-restraints excluded: chain P residue 836 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN P 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.149154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124988 restraints weight = 36510.720| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.58 r_work: 0.3455 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10196 Z= 0.175 Angle : 0.587 4.429 14269 Z= 0.338 Chirality : 0.041 0.151 1590 Planarity : 0.004 0.041 1391 Dihedral : 23.257 174.146 2476 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.01 % Allowed : 12.63 % Favored : 86.36 % 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: 0.93 (0.28), residues: 882 helix: 1.64 (0.25), residues: 381 sheet: -0.06 (0.54), residues: 81 loop : -0.13 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.022 0.001 PHE B 110 TYR 0.012 0.001 TYR P 205 ARG 0.004 0.000 ARG P 282 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 464) hydrogen bonds : angle 4.37219 ( 1220) covalent geometry : bond 0.00378 (10196) covalent geometry : angle 0.58708 (14269) *********************** 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 223 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 1.125 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 27 VAL cc_start: 0.7676 (t) cc_final: 0.7385 (t) REVERT: P 202 LYS cc_start: 0.8384 (tttt) cc_final: 0.8134 (ttpp) REVERT: P 212 THR cc_start: 0.8193 (m) cc_final: 0.7948 (p) REVERT: P 255 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8150 (mmtp) REVERT: P 331 GLU cc_start: 0.7667 (tp30) cc_final: 0.7380 (tp30) REVERT: P 380 ASP cc_start: 0.6881 (t0) cc_final: 0.6624 (t0) REVERT: P 393 LYS cc_start: 0.8450 (ptpp) cc_final: 0.8024 (mttm) REVERT: P 399 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6916 (mm-30) REVERT: P 422 LYS cc_start: 0.8491 (mttt) cc_final: 0.8238 (mttm) REVERT: P 504 LYS cc_start: 0.8499 (tttt) cc_final: 0.8238 (ttpt) REVERT: P 536 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7559 (mm-30) REVERT: P 565 LYS cc_start: 0.8480 (pttt) cc_final: 0.8251 (pttm) REVERT: P 582 GLU cc_start: 0.7697 (tp30) cc_final: 0.7481 (tm-30) REVERT: P 653 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7527 (mtp-110) REVERT: P 660 LYS cc_start: 0.8826 (tttt) cc_final: 0.8613 (tttt) REVERT: P 672 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8463 (mtpt) REVERT: P 695 LYS cc_start: 0.8060 (tppt) cc_final: 0.7461 (tptm) REVERT: P 819 ASP cc_start: 0.7973 (m-30) cc_final: 0.7614 (m-30) REVERT: P 835 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7223 (mt-10) outliers start: 8 outliers final: 6 residues processed: 219 average time/residue: 0.7242 time to fit residues: 199.6141 Evaluate side-chains 218 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.148610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124181 restraints weight = 36850.999| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.60 r_work: 0.3458 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10196 Z= 0.186 Angle : 0.574 4.274 14269 Z= 0.330 Chirality : 0.042 0.159 1590 Planarity : 0.004 0.040 1391 Dihedral : 23.143 174.021 2476 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.88 % Allowed : 13.38 % Favored : 85.73 % 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: 1.08 (0.28), residues: 882 helix: 1.87 (0.26), residues: 381 sheet: -0.10 (0.55), residues: 81 loop : -0.13 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 816 HIS 0.004 0.001 HIS B 124 PHE 0.024 0.001 PHE B 110 TYR 0.013 0.001 TYR P 141 ARG 0.005 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 464) hydrogen bonds : angle 4.27845 ( 1220) covalent geometry : bond 0.00409 (10196) covalent geometry : angle 0.57397 (14269) *********************** 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 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 1.272 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 27 VAL cc_start: 0.7666 (t) cc_final: 0.7373 (t) REVERT: P 202 LYS cc_start: 0.8384 (tttt) cc_final: 0.8145 (ttpp) REVERT: P 255 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8125 (mmtp) REVERT: P 380 ASP cc_start: 0.6845 (t0) cc_final: 0.6609 (t0) REVERT: P 393 LYS cc_start: 0.8450 (ptpp) cc_final: 0.8017 (mttm) REVERT: P 394 VAL cc_start: 0.8870 (t) cc_final: 0.8616 (m) REVERT: P 399 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6897 (mm-30) REVERT: P 422 LYS cc_start: 0.8491 (mttt) cc_final: 0.8237 (mttm) REVERT: P 504 LYS cc_start: 0.8502 (tttt) cc_final: 0.8229 (ttmm) REVERT: P 536 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7537 (mm-30) REVERT: P 565 LYS cc_start: 0.8474 (pttt) cc_final: 0.8243 (pttm) REVERT: P 582 GLU cc_start: 0.7690 (tp30) cc_final: 0.7475 (tm-30) REVERT: P 641 LYS cc_start: 0.8036 (tttt) cc_final: 0.7718 (tttt) REVERT: P 653 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7540 (mtp-110) REVERT: P 660 LYS cc_start: 0.8803 (tttt) cc_final: 0.8585 (tttt) REVERT: P 672 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8474 (mtpt) REVERT: P 695 LYS cc_start: 0.7909 (tppt) cc_final: 0.7629 (tptp) REVERT: P 786 LYS cc_start: 0.8549 (mptt) cc_final: 0.8244 (mptt) REVERT: P 819 ASP cc_start: 0.7948 (m-30) cc_final: 0.7583 (m-30) REVERT: P 835 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7249 (mt-10) outliers start: 7 outliers final: 7 residues processed: 224 average time/residue: 0.6943 time to fit residues: 196.0609 Evaluate side-chains 223 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 701 ASN Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121279 restraints weight = 36955.033| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.68 r_work: 0.3411 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 10196 Z= 0.359 Angle : 0.659 5.417 14269 Z= 0.375 Chirality : 0.050 0.200 1590 Planarity : 0.005 0.042 1391 Dihedral : 23.244 176.471 2476 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.14 % Allowed : 13.51 % Favored : 85.35 % 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: 0.61 (0.27), residues: 882 helix: 1.41 (0.25), residues: 381 sheet: -0.37 (0.51), residues: 88 loop : -0.30 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 816 HIS 0.006 0.002 HIS P 201 PHE 0.024 0.002 PHE B 110 TYR 0.024 0.002 TYR P 571 ARG 0.004 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 464) hydrogen bonds : angle 4.50669 ( 1220) covalent geometry : bond 0.00796 (10196) covalent geometry : angle 0.65915 (14269) *********************** 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 231 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 1.139 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: B 27 VAL cc_start: 0.7763 (t) cc_final: 0.7511 (t) REVERT: P 202 LYS cc_start: 0.8427 (tttt) cc_final: 0.8144 (ttpp) REVERT: P 255 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8177 (mmtp) REVERT: P 342 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: P 359 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7855 (mp0) REVERT: P 380 ASP cc_start: 0.7026 (t0) cc_final: 0.6740 (t0) REVERT: P 393 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8056 (mttm) REVERT: P 394 VAL cc_start: 0.8885 (t) cc_final: 0.8620 (m) REVERT: P 399 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6976 (mm-30) REVERT: P 422 LYS cc_start: 0.8496 (mttt) cc_final: 0.8259 (mttm) REVERT: P 504 LYS cc_start: 0.8479 (tttt) cc_final: 0.8192 (ttmm) REVERT: P 536 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7543 (mm-30) REVERT: P 565 LYS cc_start: 0.8507 (pttt) cc_final: 0.8272 (pttm) REVERT: P 582 GLU cc_start: 0.7720 (tp30) cc_final: 0.7490 (tm-30) REVERT: P 604 LEU cc_start: 0.8498 (tt) cc_final: 0.8179 (tp) REVERT: P 641 LYS cc_start: 0.8040 (tttt) cc_final: 0.7689 (tttt) REVERT: P 653 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7560 (mtp-110) REVERT: P 660 LYS cc_start: 0.8840 (tttt) cc_final: 0.8628 (tttt) REVERT: P 672 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8492 (mtpt) REVERT: P 695 LYS cc_start: 0.7864 (tppt) cc_final: 0.7577 (tptp) REVERT: P 786 LYS cc_start: 0.8569 (mptt) cc_final: 0.8268 (mptt) REVERT: P 819 ASP cc_start: 0.8021 (m-30) cc_final: 0.7739 (m-30) outliers start: 9 outliers final: 5 residues processed: 227 average time/residue: 0.7199 time to fit residues: 204.2092 Evaluate side-chains 223 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 217 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 342 GLU Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124137 restraints weight = 36759.058| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.60 r_work: 0.3449 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10196 Z= 0.180 Angle : 0.583 4.615 14269 Z= 0.335 Chirality : 0.042 0.175 1590 Planarity : 0.004 0.041 1391 Dihedral : 23.126 174.166 2476 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.76 % Allowed : 14.65 % Favored : 84.60 % 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: 0.88 (0.28), residues: 882 helix: 1.68 (0.26), residues: 381 sheet: -0.07 (0.54), residues: 81 loop : -0.25 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.022 0.001 PHE B 110 TYR 0.021 0.002 TYR P 752 ARG 0.005 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 464) hydrogen bonds : angle 4.31718 ( 1220) covalent geometry : bond 0.00397 (10196) covalent geometry : angle 0.58263 (14269) ********************** 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 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 1.198 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: B 27 VAL cc_start: 0.7706 (t) cc_final: 0.7422 (t) REVERT: B 81 PHE cc_start: 0.7826 (p90) cc_final: 0.7488 (p90) REVERT: P 202 LYS cc_start: 0.8383 (tttt) cc_final: 0.8114 (ttpp) REVERT: P 255 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8131 (mmtp) REVERT: P 359 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7842 (mp0) REVERT: P 380 ASP cc_start: 0.6860 (t0) cc_final: 0.6611 (t0) REVERT: P 393 LYS cc_start: 0.8450 (ptpp) cc_final: 0.8010 (mttm) REVERT: P 394 VAL cc_start: 0.8879 (t) cc_final: 0.8610 (m) REVERT: P 399 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6935 (mm-30) REVERT: P 422 LYS cc_start: 0.8474 (mttt) cc_final: 0.8241 (mttm) REVERT: P 504 LYS cc_start: 0.8502 (tttt) cc_final: 0.8235 (ttmm) REVERT: P 536 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7526 (mm-30) REVERT: P 565 LYS cc_start: 0.8479 (pttt) cc_final: 0.8266 (pttm) REVERT: P 582 GLU cc_start: 0.7691 (tp30) cc_final: 0.7458 (tm-30) REVERT: P 641 LYS cc_start: 0.8003 (tttt) cc_final: 0.7652 (tttt) REVERT: P 653 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7526 (mtp-110) REVERT: P 660 LYS cc_start: 0.8806 (tttt) cc_final: 0.8598 (tttt) REVERT: P 664 GLU cc_start: 0.7614 (tp30) cc_final: 0.7289 (tm-30) REVERT: P 672 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8479 (mtpt) REVERT: P 695 LYS cc_start: 0.7810 (tppt) cc_final: 0.7557 (tptp) REVERT: P 819 ASP cc_start: 0.7938 (m-30) cc_final: 0.7594 (m-30) outliers start: 6 outliers final: 5 residues processed: 225 average time/residue: 0.7209 time to fit residues: 204.4216 Evaluate side-chains 223 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 365 CYS Chi-restraints excluded: chain P residue 576 THR Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 721 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 316 ASN P 402 ASN P 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123523 restraints weight = 36702.593| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.60 r_work: 0.3441 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10196 Z= 0.219 Angle : 0.590 4.660 14269 Z= 0.340 Chirality : 0.044 0.171 1590 Planarity : 0.004 0.041 1391 Dihedral : 23.104 174.377 2476 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.01 % Allowed : 14.14 % Favored : 84.85 % 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: 0.85 (0.28), residues: 882 helix: 1.69 (0.26), residues: 381 sheet: -0.26 (0.53), residues: 80 loop : -0.26 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.022 0.001 PHE B 110 TYR 0.019 0.002 TYR P 752 ARG 0.004 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 464) hydrogen bonds : angle 4.34526 ( 1220) covalent geometry : bond 0.00484 (10196) covalent geometry : angle 0.59011 (14269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11461.23 seconds wall clock time: 195 minutes 2.55 seconds (11702.55 seconds total)