Starting phenix.real_space_refine on Thu Mar 14 16:36:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/03_2024/8jl0_36385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/03_2024/8jl0_36385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/03_2024/8jl0_36385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/03_2024/8jl0_36385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/03_2024/8jl0_36385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/03_2024/8jl0_36385_updated.pdb" } resolution = 3.1 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= 0.033 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 33 5.16 5 C 5757 2.51 5 N 1583 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9244 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4572 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3712 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 440} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "C" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'RNA': 22} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 2, 'rna3p': 19} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.56, per 1000 atoms: 0.60 Number of scatterers: 9244 At special positions: 0 Unit cell: (84.84, 115.08, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 46 15.00 O 1825 8.00 N 1583 7.00 C 5757 6.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 11 sheets defined 35.3% alpha, 12.4% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 removed outlier: 4.039A pdb=" N HIS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 4.281A pdb=" N SER A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 32' Processing helix chain 'A' and resid 37 through 49 Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.594A pdb=" N LEU A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.528A pdb=" N ALA A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 456 through 465 removed outlier: 4.913A pdb=" N ASP A 460 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 518 through 527 removed outlier: 4.003A pdb=" N THR A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASP A 522 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'B' and resid 22 through 24 No H-bonds generated for 'chain 'B' and resid 22 through 24' Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 40 through 43 removed outlier: 3.506A pdb=" N CYS B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'B' and resid 58 through 70 removed outlier: 5.143A pdb=" N ARG B 62 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 63 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 93 No H-bonds generated for 'chain 'B' and resid 90 through 93' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 110 through 118 removed outlier: 4.128A pdb=" N HIS B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.777A pdb=" N GLY B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 165 through 176 Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.698A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 294 Processing helix chain 'B' and resid 313 through 320 removed outlier: 3.615A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 removed outlier: 3.961A pdb=" N LYS B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 457 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 removed outlier: 5.847A pdb=" N GLY A 220 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE A 23 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 222 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 137 through 140 removed outlier: 6.167A pdb=" N ILE A 181 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR A 140 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA A 183 " --> pdb=" O THR A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.571A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 371 through 374 Processing sheet with id= E, first strand: chain 'A' and resid 438 through 440 removed outlier: 3.509A pdb=" N ARG A 438 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 559 through 561 Processing sheet with id= G, first strand: chain 'A' and resid 342 through 350 removed outlier: 3.674A pdb=" N ILE A 343 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 404 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 398 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 52 through 55 removed outlier: 7.115A pdb=" N VAL B 145 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU B 55 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 147 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL B 148 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN B 181 " --> pdb=" O VAL B 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 241 through 249 removed outlier: 3.852A pdb=" N SER B 228 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 246 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 226 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 328 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE B 305 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU B 330 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS B 307 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 332 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 256 through 259 removed outlier: 3.610A pdb=" N PHE B 257 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 407 through 409 removed outlier: 6.391A pdb=" N LEU B 375 " --> pdb=" O PRO B 368 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1410 1.31 - 1.43: 2851 1.43 - 1.56: 5155 1.56 - 1.69: 94 1.69 - 1.81: 51 Bond restraints: 9561 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.247 0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C4B NAD A 601 " pdb=" O4B NAD A 601 " ideal model delta sigma weight residual 1.433 1.678 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3B NAD A 601 " pdb=" C4B NAD A 601 " ideal model delta sigma weight residual 1.523 1.280 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C4D NAD A 601 " pdb=" O4D NAD A 601 " ideal model delta sigma weight residual 1.445 1.268 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C7N NAD A 601 " pdb=" N7N NAD A 601 " ideal model delta sigma weight residual 1.328 1.473 -0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 9556 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.26: 498 106.26 - 113.61: 5229 113.61 - 120.95: 4543 120.95 - 128.30: 2782 128.30 - 135.65: 116 Bond angle restraints: 13168 Sorted by residual: angle pdb=" N PRO A 329 " pdb=" CA PRO A 329 " pdb=" C PRO A 329 " ideal model delta sigma weight residual 112.47 100.45 12.02 2.06e+00 2.36e-01 3.41e+01 angle pdb=" C3' A C 1 " pdb=" O3' A C 1 " pdb=" P U C 2 " ideal model delta sigma weight residual 120.20 113.69 6.51 1.50e+00 4.44e-01 1.89e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.73 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N THR A 176 " pdb=" CA THR A 176 " pdb=" C THR A 176 " ideal model delta sigma weight residual 113.20 108.19 5.01 1.21e+00 6.83e-01 1.72e+01 angle pdb=" CA SER A 327 " pdb=" C SER A 327 " pdb=" O SER A 327 " ideal model delta sigma weight residual 121.87 117.38 4.49 1.10e+00 8.26e-01 1.67e+01 ... (remaining 13163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.70: 5099 27.70 - 55.41: 521 55.41 - 83.11: 87 83.11 - 110.81: 5 110.81 - 138.51: 2 Dihedral angle restraints: 5714 sinusoidal: 2674 harmonic: 3040 Sorted by residual: dihedral pdb=" O4' C C 17 " pdb=" C1' C C 17 " pdb=" N1 C C 17 " pdb=" C2 C C 17 " ideal model delta sinusoidal sigma weight residual -160.00 -21.49 -138.51 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" N SER A 261 " pdb=" CA SER A 261 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" C4' DC D 2 " pdb=" C3' DC D 2 " pdb=" O3' DC D 2 " pdb=" P DG D 3 " ideal model delta sinusoidal sigma weight residual -140.00 -7.37 -132.63 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 5711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1401 0.109 - 0.217: 58 0.217 - 0.326: 2 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" P A C 1 " pdb=" OP1 A C 1 " pdb=" OP2 A C 1 " pdb=" O5' A C 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" P U C 2 " pdb=" OP1 U C 2 " pdb=" OP2 U C 2 " pdb=" O5' U C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1461 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 344 " 0.444 9.50e-02 1.11e+02 1.99e-01 2.43e+01 pdb=" NE ARG A 344 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 344 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 344 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 344 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 414 " 0.016 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER A 414 " -0.052 2.00e-02 2.50e+03 pdb=" O SER A 414 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 415 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 4 " -0.033 2.00e-02 2.50e+03 1.48e-02 6.04e+00 pdb=" N9 A C 4 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A C 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A C 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A C 4 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A C 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A C 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 4 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A C 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1551 2.77 - 3.30: 8366 3.30 - 3.83: 15716 3.83 - 4.37: 18515 4.37 - 4.90: 30852 Nonbonded interactions: 75000 Sorted by model distance: nonbonded pdb=" OD1 ASN B 435 " pdb=" OG1 THR B 437 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O ALA A 578 " model vdw 2.237 2.440 nonbonded pdb=" O ARG A 440 " pdb=" OG1 THR A 443 " model vdw 2.246 2.440 nonbonded pdb=" O2D NAD A 601 " pdb=" O3D NAD A 601 " model vdw 2.257 2.432 nonbonded pdb=" OD1 ASN B 436 " pdb=" O2' A C 3 " model vdw 2.273 2.440 ... (remaining 74995 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.710 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: 3.680 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.950 Find NCS groups from input model: 0.240 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.008 0.284 9561 Z= 0.460 Angle : 0.728 12.913 13168 Z= 0.418 Chirality : 0.051 0.543 1464 Planarity : 0.006 0.199 1526 Dihedral : 20.611 138.513 3760 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.30 % Favored : 91.31 % Rotamer: Outliers : 0.79 % Allowed : 29.73 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.51 (0.25), residues: 1036 helix: 0.82 (0.28), residues: 358 sheet: -1.02 (0.37), residues: 199 loop : -2.50 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.006 0.001 HIS A 441 PHE 0.015 0.001 PHE A 91 TYR 0.015 0.002 TYR B 341 ARG 0.010 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.997 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 98 average time/residue: 0.2429 time to fit residues: 32.2528 Evaluate side-chains 89 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9561 Z= 0.187 Angle : 0.521 6.926 13168 Z= 0.278 Chirality : 0.040 0.204 1464 Planarity : 0.004 0.029 1526 Dihedral : 17.163 137.324 1788 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 3.27 % Allowed : 29.05 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1036 helix: 0.99 (0.28), residues: 358 sheet: -0.80 (0.37), residues: 199 loop : -2.44 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.004 0.001 HIS A 441 PHE 0.012 0.001 PHE A 91 TYR 0.017 0.001 TYR A 74 ARG 0.005 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.045 Fit side-chains REVERT: A 115 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.6165 (ptm160) REVERT: A 260 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7804 (mmtp) REVERT: A 426 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 221 ASP cc_start: 0.7420 (p0) cc_final: 0.7177 (p0) outliers start: 29 outliers final: 13 residues processed: 114 average time/residue: 0.2475 time to fit residues: 38.4822 Evaluate side-chains 101 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.0670 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9561 Z= 0.274 Angle : 0.564 8.004 13168 Z= 0.300 Chirality : 0.043 0.222 1464 Planarity : 0.004 0.035 1526 Dihedral : 17.251 142.482 1787 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.98 % Favored : 90.83 % Rotamer: Outliers : 4.73 % Allowed : 27.93 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.44 (0.25), residues: 1036 helix: 0.83 (0.28), residues: 359 sheet: -0.92 (0.37), residues: 200 loop : -2.45 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 377 HIS 0.005 0.001 HIS B 29 PHE 0.013 0.002 PHE A 9 TYR 0.019 0.002 TYR B 341 ARG 0.006 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 85 time to evaluate : 0.997 Fit side-chains REVERT: A 115 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.6158 (ptm160) REVERT: A 260 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7753 (mmtp) REVERT: A 426 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8043 (mp) REVERT: B 221 ASP cc_start: 0.7453 (p0) cc_final: 0.7163 (p0) outliers start: 42 outliers final: 20 residues processed: 122 average time/residue: 0.2363 time to fit residues: 39.5291 Evaluate side-chains 104 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.0010 chunk 27 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 441 HIS B 73 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9561 Z= 0.144 Angle : 0.494 8.172 13168 Z= 0.264 Chirality : 0.039 0.155 1464 Planarity : 0.004 0.031 1526 Dihedral : 16.927 134.099 1787 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.43 % Favored : 92.37 % Rotamer: Outliers : 4.62 % Allowed : 28.72 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.12 (0.26), residues: 1036 helix: 1.16 (0.28), residues: 351 sheet: -0.64 (0.38), residues: 201 loop : -2.32 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.005 0.001 HIS A 441 PHE 0.008 0.001 PHE A 80 TYR 0.012 0.001 TYR B 341 ARG 0.006 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 90 time to evaluate : 0.965 Fit side-chains REVERT: A 115 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6110 (ptm160) REVERT: A 260 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7719 (mmtp) REVERT: A 328 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.5946 (t80) REVERT: A 426 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 572 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: B 221 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7179 (p0) outliers start: 41 outliers final: 20 residues processed: 123 average time/residue: 0.2292 time to fit residues: 38.5074 Evaluate side-chains 111 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 441 HIS B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9561 Z= 0.209 Angle : 0.522 6.975 13168 Z= 0.277 Chirality : 0.041 0.166 1464 Planarity : 0.004 0.032 1526 Dihedral : 16.979 138.347 1787 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.30 % Favored : 91.51 % Rotamer: Outliers : 5.29 % Allowed : 27.82 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.26), residues: 1036 helix: 1.03 (0.28), residues: 352 sheet: -0.65 (0.38), residues: 197 loop : -2.30 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.004 0.001 HIS B 29 PHE 0.012 0.001 PHE A 91 TYR 0.016 0.001 TYR B 341 ARG 0.007 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 89 time to evaluate : 1.040 Fit side-chains REVERT: A 115 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6187 (ptm160) REVERT: A 260 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7707 (mmtp) REVERT: A 328 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5866 (t80) REVERT: A 426 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8010 (mp) REVERT: A 572 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: B 221 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7197 (p0) REVERT: B 279 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7803 (mt-10) outliers start: 47 outliers final: 26 residues processed: 128 average time/residue: 0.2176 time to fit residues: 38.3882 Evaluate side-chains 120 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 87 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9561 Z= 0.187 Angle : 0.514 6.771 13168 Z= 0.274 Chirality : 0.040 0.165 1464 Planarity : 0.004 0.035 1526 Dihedral : 16.954 137.612 1787 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.01 % Favored : 91.89 % Rotamer: Outliers : 5.29 % Allowed : 27.59 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 1036 helix: 1.06 (0.28), residues: 351 sheet: -0.64 (0.37), residues: 201 loop : -2.30 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.003 0.001 HIS B 29 PHE 0.010 0.001 PHE A 328 TYR 0.015 0.001 TYR B 341 ARG 0.006 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 85 time to evaluate : 0.794 Fit side-chains REVERT: A 46 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5539 (t70) REVERT: A 115 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.6115 (ptm160) REVERT: A 260 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7673 (mmtp) REVERT: A 328 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5788 (t80) REVERT: A 331 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8846 (tp) REVERT: A 426 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 572 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: B 176 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7226 (mp) REVERT: B 221 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7194 (p0) outliers start: 47 outliers final: 32 residues processed: 125 average time/residue: 0.2252 time to fit residues: 38.9106 Evaluate side-chains 125 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 84 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 104 GLN A 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9561 Z= 0.153 Angle : 0.490 6.208 13168 Z= 0.263 Chirality : 0.040 0.151 1464 Planarity : 0.004 0.039 1526 Dihedral : 16.835 134.415 1787 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.01 % Favored : 91.89 % Rotamer: Outliers : 5.41 % Allowed : 27.70 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.99 (0.26), residues: 1036 helix: 1.17 (0.28), residues: 352 sheet: -0.45 (0.39), residues: 194 loop : -2.20 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.003 0.001 HIS A 441 PHE 0.017 0.001 PHE A 91 TYR 0.013 0.001 TYR A 74 ARG 0.009 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 84 time to evaluate : 0.919 Fit side-chains REVERT: A 46 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5549 (t70) REVERT: A 115 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.6054 (ptm160) REVERT: A 260 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7699 (mmtp) REVERT: A 328 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5619 (t80) REVERT: A 572 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: B 221 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7213 (p0) REVERT: B 279 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7746 (mt-10) outliers start: 48 outliers final: 27 residues processed: 126 average time/residue: 0.2237 time to fit residues: 38.7586 Evaluate side-chains 119 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 85 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 441 HIS B 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9561 Z= 0.190 Angle : 0.508 6.644 13168 Z= 0.271 Chirality : 0.040 0.183 1464 Planarity : 0.004 0.039 1526 Dihedral : 16.863 136.617 1787 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.51 % Rotamer: Outliers : 4.84 % Allowed : 27.70 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.07 (0.26), residues: 1036 helix: 1.08 (0.28), residues: 352 sheet: -0.51 (0.38), residues: 197 loop : -2.23 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.003 0.001 HIS B 29 PHE 0.009 0.001 PHE A 9 TYR 0.015 0.001 TYR A 74 ARG 0.008 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 85 time to evaluate : 0.999 Fit side-chains REVERT: A 46 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5541 (t70) REVERT: A 115 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5936 (ptm160) REVERT: A 260 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7702 (mmtp) REVERT: A 328 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.5594 (t80) REVERT: A 572 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: B 176 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7245 (mp) REVERT: B 221 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7209 (p0) REVERT: B 279 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7787 (mt-10) outliers start: 43 outliers final: 31 residues processed: 122 average time/residue: 0.2433 time to fit residues: 40.5035 Evaluate side-chains 122 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 83 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.0670 chunk 98 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9561 Z= 0.152 Angle : 0.496 6.393 13168 Z= 0.265 Chirality : 0.040 0.149 1464 Planarity : 0.004 0.039 1526 Dihedral : 16.833 135.311 1787 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.92 % Favored : 91.99 % Rotamer: Outliers : 5.18 % Allowed : 27.36 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 (0.26), residues: 1036 helix: 1.10 (0.28), residues: 352 sheet: -0.45 (0.38), residues: 197 loop : -2.20 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.004 0.001 HIS A 441 PHE 0.013 0.001 PHE A 91 TYR 0.023 0.001 TYR A 271 ARG 0.009 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 83 time to evaluate : 0.869 Fit side-chains REVERT: A 46 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5546 (t70) REVERT: A 115 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5907 (ptm160) REVERT: A 260 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7689 (mmtp) REVERT: A 328 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.5549 (t80) REVERT: A 572 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: B 176 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 221 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7208 (p0) REVERT: B 256 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: B 279 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7763 (mt-10) outliers start: 46 outliers final: 34 residues processed: 123 average time/residue: 0.2256 time to fit residues: 38.2039 Evaluate side-chains 126 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 83 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9561 Z= 0.162 Angle : 0.494 6.262 13168 Z= 0.264 Chirality : 0.040 0.146 1464 Planarity : 0.004 0.041 1526 Dihedral : 16.773 134.259 1787 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.11 % Favored : 91.80 % Rotamer: Outliers : 4.73 % Allowed : 27.59 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.94 (0.26), residues: 1036 helix: 1.15 (0.29), residues: 351 sheet: -0.32 (0.40), residues: 190 loop : -2.15 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.004 0.001 HIS A 441 PHE 0.008 0.001 PHE A 328 TYR 0.024 0.001 TYR A 271 ARG 0.010 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 86 time to evaluate : 1.018 Fit side-chains REVERT: A 46 HIS cc_start: 0.5970 (OUTLIER) cc_final: 0.5549 (t70) REVERT: A 115 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5848 (ptm160) REVERT: A 260 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7680 (mmtp) REVERT: A 328 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.5485 (t80) REVERT: A 572 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: B 176 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7252 (mp) REVERT: B 221 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7207 (p0) REVERT: B 279 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7754 (mt-10) outliers start: 42 outliers final: 33 residues processed: 121 average time/residue: 0.2342 time to fit residues: 38.7750 Evaluate side-chains 122 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 81 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.0000 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122805 restraints weight = 10999.459| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.94 r_work: 0.2982 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9561 Z= 0.324 Angle : 0.587 7.690 13168 Z= 0.309 Chirality : 0.044 0.196 1464 Planarity : 0.004 0.041 1526 Dihedral : 17.068 142.864 1786 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.88 % Favored : 91.02 % Rotamer: Outliers : 4.84 % Allowed : 27.36 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1036 helix: 0.78 (0.28), residues: 353 sheet: -0.70 (0.38), residues: 199 loop : -2.26 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 377 HIS 0.006 0.001 HIS B 29 PHE 0.020 0.002 PHE A 9 TYR 0.021 0.002 TYR A 271 ARG 0.010 0.001 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.30 seconds wall clock time: 39 minutes 57.30 seconds (2397.30 seconds total)