Starting phenix.real_space_refine on Sat Sep 28 04:07:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf2_45527/09_2024/9cf2_45527.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf2_45527/09_2024/9cf2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf2_45527/09_2024/9cf2_45527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf2_45527/09_2024/9cf2_45527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf2_45527/09_2024/9cf2_45527.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cf2_45527/09_2024/9cf2_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-5461/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: 9.01, per 1000 atoms: 0.49 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: 5.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 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: 9.38 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: 6.66 Time building geometry restraints manager: 6.11 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: 6.010 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.960 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.295 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: 0.7081 time to fit residues: 251.2889 Evaluate side-chains 233 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 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 fitting. rotamer outliers: 4 poor density : 234 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: B 27 VAL cc_start: 0.7400 (t) cc_final: 0.7134 (t) REVERT: B 106 ASN cc_start: 0.7663 (m-40) cc_final: 0.7335 (m-40) REVERT: P 112 THR cc_start: 0.7663 (t) cc_final: 0.7226 (p) REVERT: P 160 PHE cc_start: 0.7647 (t80) cc_final: 0.7288 (t80) REVERT: P 202 LYS cc_start: 0.7594 (tttt) cc_final: 0.7259 (ttpp) REVERT: P 212 THR cc_start: 0.7839 (m) cc_final: 0.7480 (p) REVERT: P 331 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7029 (mt-10) REVERT: P 395 LEU cc_start: 0.8379 (tp) cc_final: 0.8177 (tt) REVERT: P 399 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6572 (mm-30) REVERT: P 422 LYS cc_start: 0.7957 (mttt) cc_final: 0.7752 (mttp) REVERT: P 504 LYS cc_start: 0.7817 (tttt) cc_final: 0.7483 (ttmm) REVERT: P 536 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6604 (mm-30) REVERT: P 556 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6947 (mt-10) REVERT: P 565 LYS cc_start: 0.7697 (pttt) cc_final: 0.7339 (pttm) REVERT: P 566 ASP cc_start: 0.7185 (m-30) cc_final: 0.6932 (m-30) REVERT: P 584 TYR cc_start: 0.8487 (m-80) cc_final: 0.8006 (m-80) REVERT: P 599 LEU cc_start: 0.7619 (tp) cc_final: 0.7416 (tt) REVERT: P 637 MET cc_start: 0.8339 (ttt) cc_final: 0.8096 (ttm) REVERT: P 653 ARG cc_start: 0.7250 (mtt180) cc_final: 0.6960 (mtp180) REVERT: P 656 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7475 (mt-10) REVERT: P 695 LYS cc_start: 0.6994 (tppt) cc_final: 0.6243 (tptm) REVERT: P 699 ASP cc_start: 0.6755 (m-30) cc_final: 0.6433 (m-30) REVERT: P 769 ASP cc_start: 0.7289 (p0) cc_final: 0.7088 (p0) REVERT: P 787 GLN cc_start: 0.7449 (mm-40) cc_final: 0.7206 (mm-40) REVERT: P 819 ASP cc_start: 0.6568 (m-30) cc_final: 0.6226 (m-30) REVERT: P 835 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6884 (mt-10) outliers start: 4 outliers final: 2 residues processed: 235 average time/residue: 0.6654 time to fit residues: 199.0599 Evaluate side-chains 220 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 218 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10196 Z= 0.337 Angle : 0.610 5.021 14269 Z= 0.351 Chirality : 0.045 0.181 1590 Planarity : 0.005 0.051 1391 Dihedral : 23.088 176.118 2476 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.52 % Allowed : 9.47 % 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: 1.55 (0.28), residues: 882 helix: 2.14 (0.26), residues: 381 sheet: 0.23 (0.53), residues: 91 loop : 0.24 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 816 HIS 0.005 0.001 HIS P 201 PHE 0.014 0.002 PHE B 111 TYR 0.017 0.002 TYR P 205 ARG 0.006 0.001 ARG B 35 *********************** 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 238 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 1.359 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: 0.7560 (t) cc_final: 0.7340 (t) REVERT: B 106 ASN cc_start: 0.7835 (m-40) cc_final: 0.7611 (m-40) REVERT: P 202 LYS cc_start: 0.7631 (tttt) cc_final: 0.7294 (ttpp) REVERT: P 212 THR cc_start: 0.7857 (m) cc_final: 0.7473 (p) REVERT: P 255 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7643 (mmtp) REVERT: P 380 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.5648 (m-30) REVERT: P 385 ASN cc_start: 0.7364 (t0) cc_final: 0.7019 (t0) REVERT: P 395 LEU cc_start: 0.8478 (tp) cc_final: 0.8237 (tt) REVERT: P 399 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6529 (mm-30) REVERT: P 422 LYS cc_start: 0.8091 (mttt) cc_final: 0.7845 (mttt) REVERT: P 504 LYS cc_start: 0.7898 (tttt) cc_final: 0.7550 (ttpt) REVERT: P 536 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6638 (mm-30) REVERT: P 556 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7031 (mt-10) REVERT: P 565 LYS cc_start: 0.7741 (pttt) cc_final: 0.7389 (pttm) REVERT: P 566 ASP cc_start: 0.7232 (m-30) cc_final: 0.6995 (m-30) REVERT: P 602 GLU cc_start: 0.6295 (pt0) cc_final: 0.6075 (pt0) REVERT: P 653 ARG cc_start: 0.7254 (mtt180) cc_final: 0.7030 (mtp180) REVERT: P 660 LYS cc_start: 0.8752 (tttt) cc_final: 0.8509 (tttt) REVERT: P 695 LYS cc_start: 0.6957 (tppt) cc_final: 0.6253 (tptm) REVERT: P 699 ASP cc_start: 0.6825 (m-30) cc_final: 0.6509 (m-30) REVERT: P 787 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7284 (mm-40) REVERT: P 819 ASP cc_start: 0.6771 (m-30) cc_final: 0.6426 (m-30) REVERT: P 835 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6892 (mt-10) outliers start: 12 outliers final: 6 residues processed: 229 average time/residue: 0.7169 time to fit residues: 208.5606 Evaluate side-chains 224 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 380 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10196 Z= 0.336 Angle : 0.605 4.837 14269 Z= 0.348 Chirality : 0.045 0.164 1590 Planarity : 0.005 0.046 1391 Dihedral : 23.219 174.848 2476 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.01 % Allowed : 10.98 % Favored : 88.01 % 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: 1.30 (0.28), residues: 882 helix: 2.01 (0.26), residues: 381 sheet: 0.14 (0.53), residues: 86 loop : -0.00 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 816 HIS 0.005 0.001 HIS P 201 PHE 0.016 0.002 PHE B 111 TYR 0.016 0.002 TYR P 141 ARG 0.005 0.000 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 229 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 221 time to evaluate : 1.194 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: 0.7581 (t) cc_final: 0.7319 (t) REVERT: P 202 LYS cc_start: 0.7642 (tttt) cc_final: 0.7360 (ttpp) REVERT: P 212 THR cc_start: 0.7872 (m) cc_final: 0.7499 (p) REVERT: P 255 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7627 (mmtp) REVERT: P 331 GLU cc_start: 0.7460 (tp30) cc_final: 0.6981 (tp30) REVERT: P 385 ASN cc_start: 0.7391 (t0) cc_final: 0.7175 (t0) REVERT: P 395 LEU cc_start: 0.8527 (tp) cc_final: 0.8272 (tt) REVERT: P 399 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6525 (mm-30) REVERT: P 504 LYS cc_start: 0.7949 (tttt) cc_final: 0.7613 (ttpt) REVERT: P 536 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6659 (mm-30) REVERT: P 556 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6990 (mt-10) REVERT: P 565 LYS cc_start: 0.7719 (pttt) cc_final: 0.7375 (pttm) REVERT: P 566 ASP cc_start: 0.7253 (m-30) cc_final: 0.7018 (m-30) REVERT: P 602 GLU cc_start: 0.6349 (pt0) cc_final: 0.6124 (pt0) REVERT: P 660 LYS cc_start: 0.8731 (tttt) cc_final: 0.8498 (tttt) REVERT: P 695 LYS cc_start: 0.6990 (tppt) cc_final: 0.6334 (tptm) REVERT: P 699 ASP cc_start: 0.6906 (m-30) cc_final: 0.6603 (m-30) REVERT: P 819 ASP cc_start: 0.6768 (m-30) cc_final: 0.6410 (m-30) REVERT: P 835 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6879 (mt-10) outliers start: 8 outliers final: 7 residues processed: 222 average time/residue: 0.7187 time to fit residues: 201.0753 Evaluate side-chains 224 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 177 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.4237 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= 0.299 Angle : 0.595 4.811 14269 Z= 0.341 Chirality : 0.043 0.159 1590 Planarity : 0.004 0.039 1391 Dihedral : 23.222 175.049 2476 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: 1.23 (0.28), residues: 882 helix: 1.92 (0.26), residues: 381 sheet: 0.14 (0.54), residues: 81 loop : -0.01 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 816 HIS 0.004 0.001 HIS P 201 PHE 0.015 0.001 PHE B 111 TYR 0.014 0.001 TYR P 141 ARG 0.004 0.000 ARG P 818 *********************** 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 fitting. 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: symmetry clash REVERT: B 27 VAL cc_start: 0.7603 (t) cc_final: 0.7328 (t) REVERT: P 202 LYS cc_start: 0.7644 (tttt) cc_final: 0.7363 (ttpp) REVERT: P 212 THR cc_start: 0.7877 (m) cc_final: 0.7523 (p) REVERT: P 255 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7632 (mmtp) REVERT: P 385 ASN cc_start: 0.7422 (t0) cc_final: 0.7138 (t0) REVERT: P 395 LEU cc_start: 0.8542 (tp) cc_final: 0.8295 (tt) REVERT: P 399 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6508 (mm-30) REVERT: P 504 LYS cc_start: 0.7982 (tttt) cc_final: 0.7631 (ttmm) REVERT: P 536 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6630 (mm-30) REVERT: P 565 LYS cc_start: 0.7728 (pttt) cc_final: 0.7407 (pttm) REVERT: P 566 ASP cc_start: 0.7255 (m-30) cc_final: 0.7017 (m-30) REVERT: P 582 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6954 (tm-30) REVERT: P 602 GLU cc_start: 0.6341 (pt0) cc_final: 0.6109 (pt0) REVERT: P 660 LYS cc_start: 0.8723 (tttt) cc_final: 0.8502 (tttt) REVERT: P 695 LYS cc_start: 0.7005 (tppt) cc_final: 0.6373 (tptm) REVERT: P 699 ASP cc_start: 0.6921 (m-30) cc_final: 0.6610 (m-30) REVERT: P 819 ASP cc_start: 0.6774 (m-30) cc_final: 0.6411 (m-30) REVERT: P 835 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6883 (mt-10) outliers start: 9 outliers final: 8 residues processed: 221 average time/residue: 0.7038 time to fit residues: 195.1986 Evaluate side-chains 223 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 215 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 177 VAL 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 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 85 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10196 Z= 0.187 Angle : 0.551 4.342 14269 Z= 0.319 Chirality : 0.040 0.154 1590 Planarity : 0.004 0.041 1391 Dihedral : 23.162 173.620 2476 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.88 % Allowed : 12.37 % Favored : 86.74 % 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: 1.40 (0.28), residues: 882 helix: 2.16 (0.26), residues: 381 sheet: 0.08 (0.53), residues: 92 loop : 0.00 (0.31), residues: 409 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 0.009 0.001 PHE B 20 TYR 0.011 0.001 TYR P 600 ARG 0.005 0.000 ARG P 282 *********************** 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 227 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 1.241 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: 0.7517 (t) cc_final: 0.7240 (t) REVERT: P 202 LYS cc_start: 0.7602 (tttt) cc_final: 0.7335 (ttpp) REVERT: P 212 THR cc_start: 0.7886 (m) cc_final: 0.7545 (p) REVERT: P 255 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7594 (mmtp) REVERT: P 385 ASN cc_start: 0.7337 (t0) cc_final: 0.7124 (t0) REVERT: P 395 LEU cc_start: 0.8501 (tp) cc_final: 0.8264 (tt) REVERT: P 399 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6407 (mm-30) REVERT: P 504 LYS cc_start: 0.7984 (tttt) cc_final: 0.7631 (ttmm) REVERT: P 536 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6582 (mm-30) REVERT: P 556 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7114 (mt-10) REVERT: P 565 LYS cc_start: 0.7714 (pttt) cc_final: 0.7395 (pttm) REVERT: P 566 ASP cc_start: 0.7234 (m-30) cc_final: 0.7000 (m-30) REVERT: P 582 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6931 (tm-30) REVERT: P 602 GLU cc_start: 0.6305 (pt0) cc_final: 0.6070 (pt0) REVERT: P 653 ARG cc_start: 0.7291 (mtp180) cc_final: 0.7074 (mtp180) REVERT: P 660 LYS cc_start: 0.8679 (tttt) cc_final: 0.8460 (tttt) REVERT: P 695 LYS cc_start: 0.6986 (tppt) cc_final: 0.6355 (tptm) REVERT: P 699 ASP cc_start: 0.6916 (m-30) cc_final: 0.6603 (m-30) REVERT: P 819 ASP cc_start: 0.6659 (m-30) cc_final: 0.6291 (m-30) REVERT: P 835 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6857 (mt-10) outliers start: 7 outliers final: 7 residues processed: 221 average time/residue: 0.7146 time to fit residues: 197.5820 Evaluate side-chains 223 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 177 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 402 ASN P 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10196 Z= 0.333 Angle : 0.600 4.655 14269 Z= 0.344 Chirality : 0.044 0.179 1590 Planarity : 0.004 0.040 1391 Dihedral : 23.186 175.148 2476 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.88 % Allowed : 12.37 % Favored : 86.74 % 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: 1.17 (0.28), residues: 882 helix: 1.96 (0.26), residues: 381 sheet: -0.08 (0.54), residues: 81 loop : -0.09 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 816 HIS 0.005 0.001 HIS P 201 PHE 0.018 0.002 PHE B 111 TYR 0.016 0.002 TYR P 141 ARG 0.005 0.001 ARG P 818 *********************** 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 fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 1.305 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: 0.7627 (t) cc_final: 0.7342 (t) REVERT: P 202 LYS cc_start: 0.7649 (tttt) cc_final: 0.7393 (ttpp) REVERT: P 212 THR cc_start: 0.7852 (m) cc_final: 0.7523 (p) REVERT: P 255 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7598 (mmtp) REVERT: P 385 ASN cc_start: 0.7420 (t0) cc_final: 0.7111 (t0) REVERT: P 393 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7902 (mttm) REVERT: P 395 LEU cc_start: 0.8556 (tp) cc_final: 0.8298 (tt) REVERT: P 399 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6456 (mm-30) REVERT: P 504 LYS cc_start: 0.7959 (tttt) cc_final: 0.7604 (ttmm) REVERT: P 536 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6632 (mm-30) REVERT: P 565 LYS cc_start: 0.7713 (pttt) cc_final: 0.7395 (pttm) REVERT: P 566 ASP cc_start: 0.7264 (m-30) cc_final: 0.7030 (m-30) REVERT: P 582 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6929 (tm-30) REVERT: P 653 ARG cc_start: 0.7377 (mtp180) cc_final: 0.7121 (mtp180) REVERT: P 660 LYS cc_start: 0.8712 (tttt) cc_final: 0.8492 (tttt) REVERT: P 695 LYS cc_start: 0.7018 (tppt) cc_final: 0.6397 (tptm) REVERT: P 699 ASP cc_start: 0.6939 (m-30) cc_final: 0.6629 (m-30) REVERT: P 819 ASP cc_start: 0.6807 (m-30) cc_final: 0.6432 (m-30) outliers start: 7 outliers final: 6 residues processed: 218 average time/residue: 0.7232 time to fit residues: 197.3544 Evaluate side-chains 220 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 214 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 721 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10196 Z= 0.320 Angle : 0.597 4.528 14269 Z= 0.343 Chirality : 0.044 0.171 1590 Planarity : 0.004 0.038 1391 Dihedral : 23.167 174.998 2476 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.88 % Allowed : 14.14 % Favored : 84.97 % 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: 1.11 (0.28), residues: 882 helix: 1.89 (0.26), residues: 381 sheet: -0.14 (0.53), residues: 83 loop : -0.11 (0.31), residues: 418 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 0.011 0.001 PHE P 415 TYR 0.022 0.002 TYR P 571 ARG 0.007 0.001 ARG P 683 *********************** 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 226 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 219 time to evaluate : 1.388 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: 0.7646 (t) cc_final: 0.7358 (t) REVERT: P 202 LYS cc_start: 0.7657 (tttt) cc_final: 0.7401 (ttpp) REVERT: P 212 THR cc_start: 0.7866 (m) cc_final: 0.7544 (p) REVERT: P 255 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7600 (mmtp) REVERT: P 385 ASN cc_start: 0.7432 (t0) cc_final: 0.7134 (t0) REVERT: P 393 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7902 (mttm) REVERT: P 394 VAL cc_start: 0.8626 (t) cc_final: 0.8308 (m) REVERT: P 395 LEU cc_start: 0.8583 (tp) cc_final: 0.8361 (tt) REVERT: P 399 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6469 (mm-30) REVERT: P 504 LYS cc_start: 0.8020 (tttt) cc_final: 0.7654 (ttmm) REVERT: P 536 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6617 (mm-30) REVERT: P 565 LYS cc_start: 0.7712 (pttt) cc_final: 0.7407 (pttm) REVERT: P 566 ASP cc_start: 0.7264 (m-30) cc_final: 0.7037 (m-30) REVERT: P 582 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6881 (tm-30) REVERT: P 604 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7599 (tp) REVERT: P 641 LYS cc_start: 0.7564 (tttt) cc_final: 0.7260 (tttt) REVERT: P 653 ARG cc_start: 0.7370 (mtp180) cc_final: 0.7126 (mtp180) REVERT: P 660 LYS cc_start: 0.8714 (tttt) cc_final: 0.8497 (tttt) REVERT: P 695 LYS cc_start: 0.7001 (tppt) cc_final: 0.6383 (tptm) REVERT: P 699 ASP cc_start: 0.6956 (m-30) cc_final: 0.6642 (m-30) REVERT: P 819 ASP cc_start: 0.6823 (m-30) cc_final: 0.6461 (m-30) outliers start: 7 outliers final: 6 residues processed: 222 average time/residue: 0.7299 time to fit residues: 204.6755 Evaluate side-chains 224 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 604 LEU 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 82 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 161 ASN P 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10196 Z= 0.190 Angle : 0.553 4.637 14269 Z= 0.319 Chirality : 0.040 0.160 1590 Planarity : 0.004 0.038 1391 Dihedral : 23.028 173.116 2476 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: 1.25 (0.29), residues: 882 helix: 2.10 (0.26), residues: 381 sheet: -0.08 (0.53), residues: 94 loop : -0.12 (0.32), residues: 407 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 0.007 0.001 PHE P 697 TYR 0.018 0.001 TYR P 752 ARG 0.006 0.000 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 226 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 1.165 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: 0.7567 (t) cc_final: 0.7279 (t) REVERT: B 109 GLN cc_start: 0.8452 (mt0) cc_final: 0.8233 (mt0) REVERT: P 202 LYS cc_start: 0.7599 (tttt) cc_final: 0.7359 (ttpp) REVERT: P 212 THR cc_start: 0.7868 (m) cc_final: 0.7551 (p) REVERT: P 255 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7566 (mmtp) REVERT: P 385 ASN cc_start: 0.7371 (t0) cc_final: 0.7118 (t0) REVERT: P 393 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7803 (mttm) REVERT: P 394 VAL cc_start: 0.8625 (t) cc_final: 0.8311 (m) REVERT: P 395 LEU cc_start: 0.8571 (tp) cc_final: 0.8369 (tt) REVERT: P 399 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6422 (mm-30) REVERT: P 504 LYS cc_start: 0.8034 (tttt) cc_final: 0.7656 (ttmm) REVERT: P 536 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6599 (mm-30) REVERT: P 565 LYS cc_start: 0.7732 (pttt) cc_final: 0.7427 (pttm) REVERT: P 566 ASP cc_start: 0.7236 (m-30) cc_final: 0.7011 (m-30) REVERT: P 582 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6855 (tm-30) REVERT: P 604 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7644 (tp) REVERT: P 641 LYS cc_start: 0.7527 (tttt) cc_final: 0.7233 (tttt) REVERT: P 653 ARG cc_start: 0.7368 (mtp180) cc_final: 0.7135 (mtp180) REVERT: P 660 LYS cc_start: 0.8663 (tttt) cc_final: 0.8459 (tttt) REVERT: P 695 LYS cc_start: 0.6981 (tppt) cc_final: 0.6733 (tptm) REVERT: P 787 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7424 (mm110) REVERT: P 819 ASP cc_start: 0.6712 (m-30) cc_final: 0.6338 (m-30) outliers start: 8 outliers final: 6 residues processed: 221 average time/residue: 0.7043 time to fit residues: 194.7853 Evaluate side-chains 224 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 154 THR Chi-restraints excluded: chain P residue 177 VAL 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 604 LEU 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 93 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 402 ASN P 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.4712 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= 0.252 Angle : 0.570 4.653 14269 Z= 0.328 Chirality : 0.042 0.160 1590 Planarity : 0.004 0.036 1391 Dihedral : 23.006 173.968 2476 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.63 % Allowed : 14.14 % Favored : 85.23 % 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: 1.18 (0.28), residues: 882 helix: 2.06 (0.26), residues: 382 sheet: -0.15 (0.54), residues: 83 loop : -0.17 (0.31), residues: 417 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 0.009 0.001 PHE B 111 TYR 0.014 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 227 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 1.162 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: 0.7593 (t) cc_final: 0.7300 (t) REVERT: P 202 LYS cc_start: 0.7620 (tttt) cc_final: 0.7377 (ttpp) REVERT: P 212 THR cc_start: 0.7885 (m) cc_final: 0.7618 (t) REVERT: P 255 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7575 (mmtp) REVERT: P 385 ASN cc_start: 0.7412 (t0) cc_final: 0.7123 (t0) REVERT: P 393 LYS cc_start: 0.8163 (ptpp) cc_final: 0.7821 (mttm) REVERT: P 394 VAL cc_start: 0.8626 (t) cc_final: 0.8305 (m) REVERT: P 395 LEU cc_start: 0.8582 (tp) cc_final: 0.8365 (tt) REVERT: P 399 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6444 (mm-30) REVERT: P 402 ASN cc_start: 0.7899 (m-40) cc_final: 0.7629 (m110) REVERT: P 504 LYS cc_start: 0.8062 (tttt) cc_final: 0.7683 (ttmm) REVERT: P 536 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6605 (mm-30) REVERT: P 565 LYS cc_start: 0.7745 (pttt) cc_final: 0.7433 (pttm) REVERT: P 566 ASP cc_start: 0.7252 (m-30) cc_final: 0.7037 (m-30) REVERT: P 604 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7622 (tp) REVERT: P 641 LYS cc_start: 0.7521 (tttt) cc_final: 0.7180 (tttt) REVERT: P 653 ARG cc_start: 0.7375 (mtp180) cc_final: 0.7153 (mtp180) REVERT: P 660 LYS cc_start: 0.8673 (tttt) cc_final: 0.8466 (tttt) REVERT: P 695 LYS cc_start: 0.6989 (tppt) cc_final: 0.6354 (tptm) REVERT: P 699 ASP cc_start: 0.6958 (m-30) cc_final: 0.6643 (m-30) REVERT: P 787 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7322 (mp10) REVERT: P 819 ASP cc_start: 0.6799 (m-30) cc_final: 0.6428 (m-30) REVERT: P 835 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6777 (mm-30) outliers start: 5 outliers final: 4 residues processed: 224 average time/residue: 0.7147 time to fit residues: 201.5541 Evaluate side-chains 225 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 220 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 604 LEU 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 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.0070 chunk 11 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.150093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125068 restraints weight = 37201.552| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.70 r_work: 0.3486 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10196 Z= 0.164 Angle : 0.540 4.913 14269 Z= 0.311 Chirality : 0.039 0.158 1590 Planarity : 0.004 0.038 1391 Dihedral : 22.883 172.258 2476 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.51 % Allowed : 14.52 % Favored : 84.97 % 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: 1.38 (0.29), residues: 882 helix: 2.29 (0.26), residues: 382 sheet: 0.02 (0.54), residues: 94 loop : -0.17 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 816 HIS 0.003 0.001 HIS B 124 PHE 0.019 0.001 PHE P 426 TYR 0.013 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: 6317.62 seconds wall clock time: 110 minutes 38.96 seconds (6638.96 seconds total)