Starting phenix.real_space_refine on Wed Jan 22 07:08:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf2_45527/01_2025/9cf2_45527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf2_45527/01_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_45527/01_2025/9cf2_45527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf2_45527/01_2025/9cf2_45527.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf2_45527/01_2025/9cf2_45527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf2_45527/01_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-5571/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: 9.19, per 1000 atoms: 0.50 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: 5.29 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: 10.29 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: 8.76 Time building geometry restraints manager: 6.21 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: 0.010 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 51.290 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: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.470 ------------------------------------------------------------------------------- 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= 0.143 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 *********************** 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 : 1.313 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: 0.7260 time to fit residues: 256.4196 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 : 1.469 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.152591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127106 restraints weight = 36869.087| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.72 r_work: 0.3516 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10196 Z= 0.291 Angle : 0.597 6.854 14269 Z= 0.346 Chirality : 0.044 0.216 1590 Planarity : 0.004 0.041 1391 Dihedral : 22.948 172.551 2476 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 8.46 % Favored : 91.04 % 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 0.006 0.001 TRP P 724 HIS 0.003 0.001 HIS P 631 PHE 0.018 0.002 PHE B 111 TYR 0.014 0.002 TYR P 141 ARG 0.005 0.001 ARG P 839 *********************** 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 : 1.329 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: 0.7326 (t) cc_final: 0.7079 (t) REVERT: B 35 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8270 (ttp80) REVERT: B 106 ASN cc_start: 0.7867 (m-40) cc_final: 0.7508 (m-40) REVERT: P 160 PHE cc_start: 0.7909 (t80) cc_final: 0.7565 (t80) REVERT: P 202 LYS cc_start: 0.8288 (tttt) cc_final: 0.7982 (ttpp) REVERT: P 212 THR cc_start: 0.8226 (m) cc_final: 0.7923 (p) REVERT: P 380 ASP cc_start: 0.6886 (t0) cc_final: 0.6631 (t0) REVERT: P 395 LEU cc_start: 0.8464 (tp) cc_final: 0.8224 (tt) REVERT: P 399 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6964 (mm-30) REVERT: P 422 LYS cc_start: 0.8445 (mttt) cc_final: 0.8185 (mttp) REVERT: P 504 LYS cc_start: 0.8308 (tttt) cc_final: 0.8034 (ttmm) REVERT: P 529 LEU cc_start: 0.8184 (mt) cc_final: 0.7911 (mp) REVERT: P 536 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7542 (mm-30) REVERT: P 565 LYS cc_start: 0.8456 (pttt) cc_final: 0.8140 (pttm) REVERT: P 584 TYR cc_start: 0.8695 (m-80) cc_final: 0.8348 (m-80) REVERT: P 637 MET cc_start: 0.8831 (ttt) cc_final: 0.8574 (ttm) REVERT: P 653 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7335 (mtp180) REVERT: P 656 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7671 (mt-10) REVERT: P 672 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8413 (mtpt) REVERT: P 695 LYS cc_start: 0.8025 (tppt) cc_final: 0.7404 (tptm) REVERT: P 699 ASP cc_start: 0.7890 (m-30) cc_final: 0.7617 (m-30) REVERT: P 784 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7437 (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: 0.7354 (m-30) REVERT: P 835 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7273 (mt-10) outliers start: 4 outliers final: 2 residues processed: 235 average time/residue: 0.7169 time to fit residues: 215.3764 Evaluate side-chains 219 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.150629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125063 restraints weight = 36747.965| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.72 r_work: 0.3481 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3426 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= 0.254 Angle : 0.577 4.809 14269 Z= 0.333 Chirality : 0.042 0.156 1590 Planarity : 0.004 0.034 1391 Dihedral : 22.990 175.333 2476 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 9.85 % 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: 2.26 (0.26), residues: 380 sheet: 0.28 (0.53), residues: 91 loop : 0.37 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.013 0.002 PHE P 254 TYR 0.014 0.001 TYR P 205 ARG 0.004 0.000 ARG P 526 *********************** 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 233 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 1.401 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 35 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8274 (ttp80) REVERT: B 106 ASN cc_start: 0.7969 (m-40) cc_final: 0.7679 (m-40) REVERT: P 114 ILE cc_start: 0.8389 (mm) cc_final: 0.8184 (tt) REVERT: P 202 LYS cc_start: 0.8304 (tttt) cc_final: 0.8015 (ttpp) REVERT: P 212 THR cc_start: 0.8232 (m) cc_final: 0.7899 (p) REVERT: P 255 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8111 (mmtp) REVERT: P 380 ASP cc_start: 0.6846 (t0) cc_final: 0.6598 (t0) REVERT: P 395 LEU cc_start: 0.8523 (tp) cc_final: 0.8265 (tt) REVERT: P 399 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6865 (mm-30) REVERT: P 422 LYS cc_start: 0.8494 (mttt) cc_final: 0.8254 (mttt) REVERT: P 504 LYS cc_start: 0.8381 (tttt) cc_final: 0.8091 (ttmm) REVERT: P 529 LEU cc_start: 0.8204 (mt) cc_final: 0.7913 (mp) REVERT: P 536 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7614 (mm-30) REVERT: P 565 LYS cc_start: 0.8470 (pttt) cc_final: 0.8206 (pttm) REVERT: P 637 MET cc_start: 0.8795 (ttt) cc_final: 0.8510 (ttm) REVERT: P 653 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7405 (mtp180) REVERT: P 656 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7762 (mt-10) REVERT: P 660 LYS cc_start: 0.8838 (tttt) cc_final: 0.8606 (tttt) REVERT: P 672 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8440 (mtpt) REVERT: P 695 LYS cc_start: 0.7993 (tppt) cc_final: 0.7361 (tptm) REVERT: P 699 ASP cc_start: 0.7963 (m-30) cc_final: 0.7681 (m-30) REVERT: P 787 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7573 (mm-40) REVERT: P 819 ASP cc_start: 0.7807 (m-30) cc_final: 0.7500 (m-30) outliers start: 9 outliers final: 5 residues processed: 226 average time/residue: 0.6873 time to fit residues: 199.9081 Evaluate side-chains 219 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 214 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 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 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: 1.9990 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: 0.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.146495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121216 restraints weight = 36817.994| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.78 r_work: 0.3418 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10196 Z= 0.409 Angle : 0.635 5.074 14269 Z= 0.364 Chirality : 0.048 0.183 1590 Planarity : 0.005 0.048 1391 Dihedral : 23.257 175.632 2476 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.26 % Allowed : 10.61 % 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: 1.19 (0.27), residues: 882 helix: 1.87 (0.26), residues: 380 sheet: -0.10 (0.51), residues: 91 loop : 0.05 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 816 HIS 0.006 0.002 HIS P 201 PHE 0.015 0.002 PHE P 235 TYR 0.018 0.002 TYR P 141 ARG 0.006 0.001 ARG P 818 *********************** 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 234 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 202 LYS cc_start: 0.8364 (tttt) cc_final: 0.8102 (ttpp) REVERT: P 212 THR cc_start: 0.8242 (m) cc_final: 0.7908 (p) REVERT: P 255 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8098 (mmtp) REVERT: P 350 LYS cc_start: 0.7424 (tptp) cc_final: 0.7223 (tptt) REVERT: P 380 ASP cc_start: 0.7026 (t0) cc_final: 0.6726 (t0) REVERT: P 395 LEU cc_start: 0.8598 (tp) cc_final: 0.8332 (tt) REVERT: P 399 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6949 (mm-30) REVERT: P 422 LYS cc_start: 0.8553 (mttt) cc_final: 0.8267 (mttm) REVERT: P 504 LYS cc_start: 0.8431 (tttt) cc_final: 0.8175 (ttpt) REVERT: P 529 LEU cc_start: 0.8204 (mt) cc_final: 0.7942 (mp) REVERT: P 536 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7595 (mm-30) REVERT: P 565 LYS cc_start: 0.8514 (pttt) cc_final: 0.8233 (pttm) REVERT: P 582 GLU cc_start: 0.7816 (tp30) cc_final: 0.7530 (tm-30) REVERT: P 602 GLU cc_start: 0.6815 (pt0) cc_final: 0.6592 (pt0) REVERT: P 636 ILE cc_start: 0.8607 (mt) cc_final: 0.8404 (tt) REVERT: P 653 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7490 (mtp180) REVERT: P 660 LYS cc_start: 0.8864 (tttt) cc_final: 0.8625 (tttt) REVERT: P 672 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8463 (mtpt) REVERT: P 695 LYS cc_start: 0.8069 (tppt) cc_final: 0.7550 (tptm) REVERT: P 699 ASP cc_start: 0.7990 (m-30) cc_final: 0.7743 (m-30) REVERT: P 819 ASP cc_start: 0.7964 (m-30) cc_final: 0.7626 (m-30) REVERT: P 835 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7299 (mt-10) outliers start: 10 outliers final: 8 residues processed: 227 average time/residue: 0.7297 time to fit residues: 209.6316 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 : 1.239 ------------------------------------------------------------------------------- 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 507 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.148843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123936 restraints weight = 36529.726| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.64 r_work: 0.3474 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10196 Z= 0.225 Angle : 0.571 4.938 14269 Z= 0.329 Chirality : 0.041 0.148 1590 Planarity : 0.004 0.048 1391 Dihedral : 23.181 174.211 2476 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 1.32 (0.28), residues: 882 helix: 2.05 (0.26), residues: 381 sheet: -0.07 (0.52), residues: 86 loop : 0.04 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.021 0.001 PHE B 110 TYR 0.012 0.001 TYR P 141 ARG 0.007 0.000 ARG B 35 *********************** 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 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 1.265 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: 0.7605 (t) cc_final: 0.7336 (t) REVERT: P 202 LYS cc_start: 0.8357 (tttt) cc_final: 0.8097 (ttpp) REVERT: P 212 THR cc_start: 0.8300 (m) cc_final: 0.8019 (p) REVERT: P 255 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8185 (mmtp) REVERT: P 380 ASP cc_start: 0.6855 (t0) cc_final: 0.6653 (t0) REVERT: P 395 LEU cc_start: 0.8559 (tp) cc_final: 0.8344 (tt) REVERT: P 399 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6849 (mm-30) REVERT: P 422 LYS cc_start: 0.8504 (mttt) cc_final: 0.8246 (mttm) REVERT: P 504 LYS cc_start: 0.8484 (tttt) cc_final: 0.8216 (ttmm) REVERT: P 529 LEU cc_start: 0.8262 (mt) cc_final: 0.7987 (mp) REVERT: P 536 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7572 (mm-30) REVERT: P 565 LYS cc_start: 0.8479 (pttt) cc_final: 0.8242 (pttm) REVERT: P 582 GLU cc_start: 0.7776 (tp30) cc_final: 0.7467 (tm-30) REVERT: P 602 GLU cc_start: 0.6678 (pt0) cc_final: 0.6473 (pt0) REVERT: P 660 LYS cc_start: 0.8824 (tttt) cc_final: 0.8605 (tttt) REVERT: P 672 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8471 (mtpt) REVERT: P 695 LYS cc_start: 0.8078 (tppt) cc_final: 0.7508 (tptm) REVERT: P 699 ASP cc_start: 0.7966 (m-30) cc_final: 0.7702 (m-30) REVERT: P 819 ASP cc_start: 0.7887 (m-30) cc_final: 0.7555 (m-30) REVERT: P 835 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7204 (mt-10) outliers start: 9 outliers final: 7 residues processed: 220 average time/residue: 0.7503 time to fit residues: 207.2499 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 : 1.313 ------------------------------------------------------------------------------- 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 303 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 729 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: 0.1980 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: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.146409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122323 restraints weight = 36936.804| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.67 r_work: 0.3424 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 10196 Z= 0.459 Angle : 0.660 5.541 14269 Z= 0.375 Chirality : 0.049 0.198 1590 Planarity : 0.005 0.052 1391 Dihedral : 23.375 176.395 2476 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.52 % Allowed : 11.36 % 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: 0.89 (0.27), residues: 882 helix: 1.61 (0.25), residues: 381 sheet: -0.22 (0.52), residues: 86 loop : -0.12 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 816 HIS 0.006 0.002 HIS P 201 PHE 0.021 0.002 PHE B 110 TYR 0.019 0.002 TYR P 141 ARG 0.007 0.001 ARG P 818 *********************** 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 233 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 1.551 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: 0.7755 (t) cc_final: 0.7481 (t) REVERT: P 106 ARG cc_start: 0.7018 (ttt-90) cc_final: 0.6784 (ttt-90) REVERT: P 202 LYS cc_start: 0.8417 (tttt) cc_final: 0.8138 (ttpp) REVERT: P 212 THR cc_start: 0.8300 (m) cc_final: 0.8021 (p) REVERT: P 255 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8193 (mmtp) REVERT: P 342 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: P 380 ASP cc_start: 0.7031 (t0) cc_final: 0.6743 (t0) REVERT: P 393 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8009 (mttm) REVERT: P 395 LEU cc_start: 0.8632 (tp) cc_final: 0.8416 (tt) REVERT: P 399 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7008 (mm-30) REVERT: P 422 LYS cc_start: 0.8478 (mttt) cc_final: 0.8219 (mttm) REVERT: P 504 LYS cc_start: 0.8490 (tttt) cc_final: 0.8213 (ttmm) REVERT: P 536 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7554 (mm-30) REVERT: P 565 LYS cc_start: 0.8470 (pttt) cc_final: 0.8237 (pttm) REVERT: P 582 GLU cc_start: 0.7798 (tp30) cc_final: 0.7473 (tm-30) REVERT: P 602 GLU cc_start: 0.6794 (pt0) cc_final: 0.6563 (pt0) REVERT: P 604 LEU cc_start: 0.8438 (tt) cc_final: 0.8112 (tp) REVERT: P 660 LYS cc_start: 0.8855 (tttt) cc_final: 0.8626 (tttt) REVERT: P 672 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8476 (mtpt) REVERT: P 695 LYS cc_start: 0.8127 (tppt) cc_final: 0.7581 (tptm) REVERT: P 699 ASP cc_start: 0.7971 (m-30) cc_final: 0.7718 (m-30) REVERT: P 701 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7723 (t0) REVERT: P 786 LYS cc_start: 0.8591 (mptt) cc_final: 0.8272 (mptt) REVERT: P 819 ASP cc_start: 0.8012 (m-30) cc_final: 0.7688 (m-30) REVERT: P 835 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7232 (mt-10) outliers start: 12 outliers final: 8 residues processed: 229 average time/residue: 0.7359 time to fit residues: 211.2448 Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 303 GLU 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 701 ASN Chi-restraints excluded: chain P residue 721 LEU 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: 0.4980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN ** P 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124526 restraints weight = 36595.902| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.61 r_work: 0.3457 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10196 Z= 0.222 Angle : 0.578 4.352 14269 Z= 0.333 Chirality : 0.041 0.150 1590 Planarity : 0.005 0.052 1391 Dihedral : 23.223 174.115 2476 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.26 % Allowed : 12.37 % 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: 1.02 (0.28), residues: 882 helix: 1.76 (0.25), residues: 381 sheet: -0.11 (0.54), residues: 81 loop : -0.10 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.018 0.001 PHE B 110 TYR 0.015 0.001 TYR P 752 ARG 0.004 0.000 ARG P 282 *********************** 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 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 1.209 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: 0.7625 (t) cc_final: 0.7342 (t) REVERT: P 202 LYS cc_start: 0.8382 (tttt) cc_final: 0.8136 (ttpp) REVERT: P 212 THR cc_start: 0.8275 (m) cc_final: 0.8008 (p) REVERT: P 255 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8125 (mmtp) REVERT: P 380 ASP cc_start: 0.6886 (t0) cc_final: 0.6635 (t0) REVERT: P 393 LYS cc_start: 0.8436 (ptpp) cc_final: 0.7987 (mttm) REVERT: P 395 LEU cc_start: 0.8618 (tp) cc_final: 0.8386 (tt) REVERT: P 399 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6859 (mm-30) REVERT: P 422 LYS cc_start: 0.8467 (mttt) cc_final: 0.8208 (mttm) REVERT: P 504 LYS cc_start: 0.8479 (tttt) cc_final: 0.8205 (ttmm) REVERT: P 536 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7531 (mm-30) REVERT: P 565 LYS cc_start: 0.8476 (pttt) cc_final: 0.8242 (pttm) REVERT: P 582 GLU cc_start: 0.7794 (tp30) cc_final: 0.7443 (tm-30) REVERT: P 602 GLU cc_start: 0.6730 (pt0) cc_final: 0.6489 (pt0) REVERT: P 653 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7621 (mtp180) REVERT: P 660 LYS cc_start: 0.8798 (tttt) cc_final: 0.8584 (tttt) REVERT: P 672 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8479 (mtpt) REVERT: P 695 LYS cc_start: 0.8049 (tppt) cc_final: 0.7485 (tptm) REVERT: P 699 ASP cc_start: 0.7974 (m-30) cc_final: 0.7727 (m-30) REVERT: P 786 LYS cc_start: 0.8574 (mptt) cc_final: 0.8241 (mptt) REVERT: P 819 ASP cc_start: 0.7966 (m-30) cc_final: 0.7600 (m-30) REVERT: P 835 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7232 (mt-10) outliers start: 10 outliers final: 8 residues processed: 221 average time/residue: 0.7555 time to fit residues: 209.4664 Evaluate side-chains 224 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain P residue 303 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.149222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124927 restraints weight = 36864.593| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.60 r_work: 0.3461 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10196 Z= 0.221 Angle : 0.562 4.512 14269 Z= 0.323 Chirality : 0.041 0.148 1590 Planarity : 0.004 0.040 1391 Dihedral : 23.100 173.633 2476 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.14 % Allowed : 13.01 % Favored : 85.86 % 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: 1.20 (0.28), residues: 882 helix: 2.00 (0.26), residues: 381 sheet: -0.02 (0.55), residues: 81 loop : -0.11 (0.31), residues: 420 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 0.018 0.001 PHE B 110 TYR 0.012 0.001 TYR P 141 ARG 0.006 0.000 ARG P 282 *********************** 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 234 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 1.743 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: 0.7628 (t) cc_final: 0.7340 (t) REVERT: P 202 LYS cc_start: 0.8359 (tttt) cc_final: 0.8128 (ttpp) REVERT: P 212 THR cc_start: 0.8242 (m) cc_final: 0.7983 (p) REVERT: P 255 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8127 (mmtp) REVERT: P 380 ASP cc_start: 0.6826 (t0) cc_final: 0.6617 (t0) REVERT: P 393 LYS cc_start: 0.8429 (ptpp) cc_final: 0.7994 (mttm) REVERT: P 395 LEU cc_start: 0.8610 (tp) cc_final: 0.8388 (tt) REVERT: P 399 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6821 (mm-30) REVERT: P 422 LYS cc_start: 0.8463 (mttt) cc_final: 0.8216 (mttm) REVERT: P 504 LYS cc_start: 0.8471 (tttt) cc_final: 0.8205 (ttmm) REVERT: P 536 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7530 (mm-30) REVERT: P 565 LYS cc_start: 0.8466 (pttt) cc_final: 0.8235 (pttm) REVERT: P 582 GLU cc_start: 0.7786 (tp30) cc_final: 0.7532 (tm-30) REVERT: P 602 GLU cc_start: 0.6681 (pt0) cc_final: 0.6439 (pt0) REVERT: P 641 LYS cc_start: 0.8019 (tttt) cc_final: 0.7699 (tttt) REVERT: P 653 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7620 (mtp180) REVERT: P 660 LYS cc_start: 0.8784 (tttt) cc_final: 0.8568 (tttt) REVERT: P 672 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8462 (mtpt) REVERT: P 695 LYS cc_start: 0.8082 (tppt) cc_final: 0.7498 (tptm) REVERT: P 699 ASP cc_start: 0.7978 (m-30) cc_final: 0.7754 (m-30) REVERT: P 786 LYS cc_start: 0.8558 (mptt) cc_final: 0.8247 (mptt) REVERT: P 819 ASP cc_start: 0.7920 (m-30) cc_final: 0.7533 (m-30) REVERT: P 835 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7231 (mt-10) outliers start: 9 outliers final: 8 residues processed: 228 average time/residue: 0.7617 time to fit residues: 219.3281 Evaluate side-chains 228 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain P residue 303 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=1.50 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.7980 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.147265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122962 restraints weight = 36843.129| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.64 r_work: 0.3428 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10196 Z= 0.376 Angle : 0.617 5.043 14269 Z= 0.353 Chirality : 0.046 0.182 1590 Planarity : 0.004 0.039 1391 Dihedral : 23.156 175.201 2476 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.14 % Allowed : 12.50 % 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: 0.90 (0.28), residues: 882 helix: 1.72 (0.26), residues: 381 sheet: -0.32 (0.52), residues: 88 loop : -0.19 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 816 HIS 0.005 0.001 HIS P 201 PHE 0.017 0.002 PHE B 110 TYR 0.022 0.002 TYR P 752 ARG 0.004 0.001 ARG B 35 *********************** 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 232 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 1.215 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: 0.7678 (t) cc_final: 0.7396 (t) REVERT: B 81 PHE cc_start: 0.7821 (p90) cc_final: 0.7466 (p90) REVERT: P 202 LYS cc_start: 0.8406 (tttt) cc_final: 0.8123 (ttpp) REVERT: P 212 THR cc_start: 0.8239 (m) cc_final: 0.7976 (p) REVERT: P 255 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8154 (mmtp) REVERT: P 380 ASP cc_start: 0.6949 (t0) cc_final: 0.6674 (t0) REVERT: P 393 LYS cc_start: 0.8433 (ptpp) cc_final: 0.7998 (mttm) REVERT: P 394 VAL cc_start: 0.8860 (t) cc_final: 0.8596 (m) REVERT: P 395 LEU cc_start: 0.8644 (tp) cc_final: 0.8436 (tt) REVERT: P 399 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6903 (mm-30) REVERT: P 422 LYS cc_start: 0.8476 (mttt) cc_final: 0.8232 (mttm) REVERT: P 504 LYS cc_start: 0.8464 (tttt) cc_final: 0.8177 (ttmm) REVERT: P 536 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7526 (mm-30) REVERT: P 565 LYS cc_start: 0.8513 (pttt) cc_final: 0.8280 (pttm) REVERT: P 582 GLU cc_start: 0.7803 (tp30) cc_final: 0.7535 (tm-30) REVERT: P 602 GLU cc_start: 0.6754 (pt0) cc_final: 0.6518 (pt0) REVERT: P 641 LYS cc_start: 0.8012 (tttt) cc_final: 0.7661 (tttt) REVERT: P 653 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7650 (mtp180) REVERT: P 660 LYS cc_start: 0.8816 (tttt) cc_final: 0.8603 (tttt) REVERT: P 672 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8490 (mtpt) REVERT: P 695 LYS cc_start: 0.8054 (tppt) cc_final: 0.7504 (tptm) REVERT: P 699 ASP cc_start: 0.8023 (m-30) cc_final: 0.7766 (m-30) REVERT: P 786 LYS cc_start: 0.8580 (mptt) cc_final: 0.8272 (mptt) REVERT: P 819 ASP cc_start: 0.8010 (m-30) cc_final: 0.7659 (m-30) outliers start: 9 outliers final: 8 residues processed: 227 average time/residue: 0.7762 time to fit residues: 222.0243 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 : 1.262 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain P residue 303 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: 0.1980 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 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: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.149195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124894 restraints weight = 36748.735| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.60 r_work: 0.3465 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10196 Z= 0.209 Angle : 0.567 4.787 14269 Z= 0.326 Chirality : 0.041 0.188 1590 Planarity : 0.004 0.039 1391 Dihedral : 23.034 173.462 2476 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.88 % Allowed : 13.13 % Favored : 85.98 % 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: 1.09 (0.28), residues: 882 helix: 1.94 (0.26), residues: 381 sheet: -0.19 (0.54), residues: 83 loop : -0.17 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.015 0.001 PHE B 110 TYR 0.018 0.001 TYR P 571 ARG 0.005 0.000 ARG B 35 ********************** 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 226 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 1.437 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 27 VAL cc_start: 0.7649 (t) cc_final: 0.7351 (t) REVERT: P 202 LYS cc_start: 0.8372 (tttt) cc_final: 0.8141 (ttpp) REVERT: P 255 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8135 (mmtp) REVERT: P 393 LYS cc_start: 0.8439 (ptpp) cc_final: 0.7983 (mttm) REVERT: P 395 LEU cc_start: 0.8614 (tp) cc_final: 0.8389 (tt) REVERT: P 399 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6853 (mm-30) REVERT: P 422 LYS cc_start: 0.8470 (mttt) cc_final: 0.8233 (mttm) REVERT: P 440 LEU cc_start: 0.8745 (mt) cc_final: 0.8479 (mt) REVERT: P 504 LYS cc_start: 0.8500 (tttt) cc_final: 0.8232 (ttmm) REVERT: P 536 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7535 (mm-30) REVERT: P 565 LYS cc_start: 0.8486 (pttt) cc_final: 0.8260 (pttm) REVERT: P 582 GLU cc_start: 0.7759 (tp30) cc_final: 0.7491 (tm-30) REVERT: P 602 GLU cc_start: 0.6664 (pt0) cc_final: 0.6433 (pt0) REVERT: P 641 LYS cc_start: 0.7980 (tttt) cc_final: 0.7630 (tttt) REVERT: P 653 ARG cc_start: 0.7848 (mtp180) cc_final: 0.7641 (mtp180) REVERT: P 660 LYS cc_start: 0.8774 (tttt) cc_final: 0.8571 (tttt) REVERT: P 664 GLU cc_start: 0.7586 (tp30) cc_final: 0.7266 (tm-30) REVERT: P 672 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8470 (mtpt) REVERT: P 695 LYS cc_start: 0.8021 (tppt) cc_final: 0.7778 (tptm) REVERT: P 787 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7695 (mm-40) REVERT: P 819 ASP cc_start: 0.7927 (m-30) cc_final: 0.7567 (m-30) outliers start: 7 outliers final: 7 residues processed: 221 average time/residue: 0.7808 time to fit residues: 216.3840 Evaluate side-chains 222 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 263 LEU Chi-restraints excluded: chain P residue 303 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 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 353 GLN P 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123575 restraints weight = 37242.070| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.68 r_work: 0.3438 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10196 Z= 0.269 Angle : 0.581 5.445 14269 Z= 0.333 Chirality : 0.043 0.173 1590 Planarity : 0.004 0.037 1391 Dihedral : 23.009 173.998 2476 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.01 % Allowed : 13.26 % 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: 1.03 (0.28), residues: 882 helix: 1.92 (0.26), residues: 382 sheet: -0.18 (0.54), residues: 83 loop : -0.26 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 816 HIS 0.005 0.001 HIS B 124 PHE 0.012 0.001 PHE B 110 TYR 0.018 0.001 TYR P 571 ARG 0.005 0.000 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11296.63 seconds wall clock time: 200 minutes 47.48 seconds (12047.48 seconds total)