Starting phenix.real_space_refine on Mon Mar 11 06:44:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffy_29070/03_2024/8ffy_29070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffy_29070/03_2024/8ffy_29070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffy_29070/03_2024/8ffy_29070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffy_29070/03_2024/8ffy_29070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffy_29070/03_2024/8ffy_29070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffy_29070/03_2024/8ffy_29070_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.011 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 61 5.49 5 S 34 5.16 5 C 4455 2.51 5 N 1333 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A ARG 415": "NH1" <-> "NH2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 415": "NH1" <-> "NH2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ASP 472": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7442 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2493 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3590 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 424} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1301 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 54} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.68 Number of scatterers: 7442 At special positions: 0 Unit cell: (105.8, 80.5, 113.85, 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 34 16.00 P 61 15.00 O 1559 8.00 N 1333 7.00 C 4455 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: 3.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 6 sheets defined 35.2% alpha, 15.2% beta 20 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.579A pdb=" N TYR A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 382 Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 457 through 467 Processing helix chain 'A' and resid 482 through 485 No H-bonds generated for 'chain 'A' and resid 482 through 485' Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 86 through 120 Processing helix chain 'B' and resid 133 through 167 Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 234 through 253 removed outlier: 3.697A pdb=" N ARG B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 361 through 382 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'B' and resid 482 through 485 No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 265 Processing sheet with id= B, first strand: chain 'A' and resid 320 through 329 removed outlier: 5.828A pdb=" N MET A 353 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR A 453 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 355 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASN A 451 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A 357 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR A 449 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 192 removed outlier: 7.069A pdb=" N VAL A 388 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N MET A 191 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE A 386 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 402 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA A 408 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU A 418 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 436 through 438 Processing sheet with id= E, first strand: chain 'B' and resid 256 through 258 removed outlier: 4.565A pdb=" N SER B 325 " --> pdb=" O MET B 258 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 455 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET B 353 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR B 453 " --> pdb=" O MET B 353 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLY B 355 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASN B 451 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR B 357 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N THR B 449 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER B 421 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS B 455 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N VAL B 419 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 415 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B 410 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 406 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER B 421 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 404 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER B 423 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG B 402 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS B 190 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP B 390 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 188 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 436 through 438 232 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2124 1.34 - 1.45: 1565 1.45 - 1.57: 3860 1.57 - 1.69: 128 1.69 - 1.81: 56 Bond restraints: 7733 Sorted by residual: bond pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.13e+01 bond pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" O5' SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.581 1.735 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" O5' SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.581 1.733 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" O2S SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.435 1.586 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 7728 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.39: 643 107.39 - 114.03: 4429 114.03 - 120.67: 3130 120.67 - 127.31: 2376 127.31 - 133.94: 192 Bond angle restraints: 10770 Sorted by residual: angle pdb=" C3' U C 72 " pdb=" O3' U C 72 " pdb=" P G C 73 " ideal model delta sigma weight residual 120.20 109.80 10.40 1.50e+00 4.44e-01 4.80e+01 angle pdb=" O1S SSA B 601 " pdb=" S1 SSA B 601 " pdb=" O2S SSA B 601 " ideal model delta sigma weight residual 121.34 101.15 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O1S SSA A 601 " pdb=" S1 SSA A 601 " pdb=" O2S SSA A 601 " ideal model delta sigma weight residual 121.34 101.15 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" C3' U C 71 " pdb=" O3' U C 71 " pdb=" P U C 72 " ideal model delta sigma weight residual 120.20 111.06 9.14 1.50e+00 4.44e-01 3.71e+01 angle pdb=" C HIS A 226 " pdb=" N ARG A 227 " pdb=" CA ARG A 227 " ideal model delta sigma weight residual 122.93 113.99 8.94 1.51e+00 4.39e-01 3.51e+01 ... (remaining 10765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 4495 32.51 - 65.02: 267 65.02 - 97.54: 37 97.54 - 130.05: 0 130.05 - 162.56: 1 Dihedral angle restraints: 4800 sinusoidal: 2589 harmonic: 2211 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 232.00 162.24 69.76 1 1.70e+01 3.46e-03 2.17e+01 dihedral pdb=" C5' U C 9 " pdb=" C4' U C 9 " pdb=" C3' U C 9 " pdb=" O3' U C 9 " ideal model delta sinusoidal sigma weight residual 147.00 116.13 30.87 1 8.00e+00 1.56e-02 2.12e+01 dihedral pdb=" C3' U C 9 " pdb=" C4' U C 9 " pdb=" O4' U C 9 " pdb=" C1' U C 9 " ideal model delta sinusoidal sigma weight residual -2.00 24.84 -26.84 1 8.00e+00 1.56e-02 1.62e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1193 0.110 - 0.220: 36 0.220 - 0.329: 0 0.329 - 0.439: 3 0.439 - 0.549: 3 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CA SSA A 601 " pdb=" CB SSA A 601 " pdb=" C9 SSA A 601 " pdb=" N10 SSA A 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.02 0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CA SSA B 601 " pdb=" CB SSA B 601 " pdb=" C9 SSA B 601 " pdb=" N10 SSA B 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.01 0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" P U C 71 " pdb=" OP1 U C 71 " pdb=" OP2 U C 71 " pdb=" O5' U C 71 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.54e+00 ... (remaining 1232 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 226 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C HIS A 226 " -0.038 2.00e-02 2.50e+03 pdb=" O HIS A 226 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 227 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 71 " -0.012 2.00e-02 2.50e+03 1.25e-02 3.50e+00 pdb=" N1 U C 71 " 0.018 2.00e-02 2.50e+03 pdb=" C2 U C 71 " 0.020 2.00e-02 2.50e+03 pdb=" O2 U C 71 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U C 71 " -0.011 2.00e-02 2.50e+03 pdb=" C4 U C 71 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U C 71 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U C 71 " 0.012 2.00e-02 2.50e+03 pdb=" C6 U C 71 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 457 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO B 458 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.020 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 213 2.68 - 3.24: 6914 3.24 - 3.79: 12271 3.79 - 4.35: 15997 4.35 - 4.90: 25113 Nonbonded interactions: 60508 Sorted by model distance: nonbonded pdb=" OG1 THR A 333 " pdb=" OP2 G C 1 " model vdw 2.125 2.440 nonbonded pdb=" OE2 GLU A 352 " pdb=" OG SSA A 601 " model vdw 2.127 2.440 nonbonded pdb=" OE2 GLU B 352 " pdb=" OG SSA B 601 " model vdw 2.144 2.440 nonbonded pdb=" OE2 GLU A 352 " pdb=" N10 SSA A 601 " model vdw 2.243 2.520 nonbonded pdb=" O GLU B 418 " pdb=" NH1 ARG B 459 " model vdw 2.246 2.520 ... (remaining 60503 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 group one per residue 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: 0.320 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: 0.010 Extract box with map and model: 1.970 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.740 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 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 0.191 7733 Z= 0.451 Angle : 0.718 20.191 10770 Z= 0.366 Chirality : 0.050 0.549 1235 Planarity : 0.003 0.036 1178 Dihedral : 19.051 162.558 3378 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.66 (0.29), residues: 760 helix: 1.87 (0.30), residues: 285 sheet: -1.42 (0.46), residues: 105 loop : -2.11 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 409 HIS 0.002 0.000 HIS A 347 PHE 0.007 0.000 PHE A 348 TYR 0.006 0.000 TYR B 230 ARG 0.005 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7346 (mtt180) cc_final: 0.7135 (mtm-85) REVERT: A 218 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7629 (mmmt) REVERT: A 244 ASN cc_start: 0.7760 (m-40) cc_final: 0.7385 (m110) REVERT: A 366 GLN cc_start: 0.7153 (pt0) cc_final: 0.6864 (tm-30) REVERT: A 438 GLN cc_start: 0.8244 (tt0) cc_final: 0.8043 (tt0) REVERT: A 451 ASN cc_start: 0.7540 (p0) cc_final: 0.6953 (p0) REVERT: A 460 LEU cc_start: 0.7512 (mm) cc_final: 0.7277 (mm) REVERT: A 466 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6031 (mt-10) REVERT: B 143 ARG cc_start: 0.6815 (mmm-85) cc_final: 0.5986 (ttm170) REVERT: B 203 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7094 (mtm-85) REVERT: B 313 VAL cc_start: 0.8292 (t) cc_final: 0.8066 (m) REVERT: B 332 GLU cc_start: 0.7442 (tp30) cc_final: 0.7221 (mm-30) REVERT: B 451 ASN cc_start: 0.8027 (p0) cc_final: 0.7425 (p0) REVERT: B 499 GLN cc_start: 0.7939 (tp40) cc_final: 0.7269 (tt0) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2510 time to fit residues: 66.0525 Evaluate side-chains 113 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 217 GLN A 346 HIS A 495 HIS B 448 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 7733 Z= 0.466 Angle : 0.735 7.357 10770 Z= 0.366 Chirality : 0.045 0.202 1235 Planarity : 0.005 0.045 1178 Dihedral : 19.066 177.197 1891 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.86 % Allowed : 17.10 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.67 (0.30), residues: 760 helix: 1.41 (0.31), residues: 286 sheet: -0.50 (0.48), residues: 100 loop : -2.01 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP B 93 HIS 0.007 0.002 HIS A 385 PHE 0.017 0.003 PHE B 63 TYR 0.022 0.003 TYR B 401 ARG 0.010 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7193 (mtm-85) REVERT: A 207 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6815 (tm-30) REVERT: A 301 GLU cc_start: 0.6997 (tt0) cc_final: 0.6786 (tt0) REVERT: A 366 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: A 438 GLN cc_start: 0.8356 (tt0) cc_final: 0.8089 (tt0) REVERT: B 143 ARG cc_start: 0.6704 (mmm-85) cc_final: 0.5859 (ttm170) REVERT: B 203 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7699 (mtm-85) REVERT: B 258 MET cc_start: 0.8298 (ttt) cc_final: 0.8076 (ttm) REVERT: B 398 LEU cc_start: 0.8275 (mm) cc_final: 0.8049 (mt) outliers start: 38 outliers final: 27 residues processed: 139 average time/residue: 0.2495 time to fit residues: 44.5215 Evaluate side-chains 119 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7733 Z= 0.184 Angle : 0.509 6.595 10770 Z= 0.255 Chirality : 0.037 0.168 1235 Planarity : 0.004 0.031 1178 Dihedral : 18.788 175.197 1891 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.24 % Allowed : 18.49 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.03 (0.30), residues: 760 helix: 2.02 (0.31), residues: 281 sheet: 0.13 (0.49), residues: 99 loop : -1.74 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 409 HIS 0.006 0.001 HIS A 190 PHE 0.011 0.001 PHE A 371 TYR 0.013 0.001 TYR B 45 ARG 0.003 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 0.768 Fit side-chains REVERT: A 203 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7185 (mtm-85) REVERT: A 207 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 252 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: A 291 PHE cc_start: 0.6859 (m-80) cc_final: 0.6640 (m-10) REVERT: A 301 GLU cc_start: 0.7023 (tt0) cc_final: 0.6794 (tt0) REVERT: A 322 MET cc_start: 0.7356 (mpp) cc_final: 0.7101 (mtt) REVERT: A 366 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: A 438 GLN cc_start: 0.8372 (tt0) cc_final: 0.8131 (tt0) REVERT: B 143 ARG cc_start: 0.6700 (mmm-85) cc_final: 0.5749 (ttm170) REVERT: B 191 MET cc_start: 0.8525 (tpp) cc_final: 0.8295 (tpp) outliers start: 34 outliers final: 21 residues processed: 117 average time/residue: 0.2277 time to fit residues: 34.6064 Evaluate side-chains 106 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7733 Z= 0.354 Angle : 0.607 6.770 10770 Z= 0.305 Chirality : 0.041 0.172 1235 Planarity : 0.004 0.032 1178 Dihedral : 18.918 175.873 1891 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 6.78 % Allowed : 17.26 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.32 (0.30), residues: 760 helix: 1.72 (0.31), residues: 284 sheet: -0.24 (0.50), residues: 109 loop : -1.86 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 409 HIS 0.005 0.001 HIS A 385 PHE 0.014 0.002 PHE B 63 TYR 0.023 0.002 TYR B 45 ARG 0.004 0.001 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 92 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7181 (mtm-85) REVERT: A 207 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6500 (tm-30) REVERT: A 301 GLU cc_start: 0.7249 (tt0) cc_final: 0.7002 (tt0) REVERT: A 350 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7930 (ptmt) REVERT: A 366 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: B 82 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7291 (mmm160) REVERT: B 83 SER cc_start: 0.8404 (t) cc_final: 0.8188 (t) outliers start: 44 outliers final: 34 residues processed: 125 average time/residue: 0.2125 time to fit residues: 35.0334 Evaluate side-chains 120 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7733 Z= 0.261 Angle : 0.535 6.828 10770 Z= 0.268 Chirality : 0.038 0.168 1235 Planarity : 0.004 0.034 1178 Dihedral : 18.873 175.198 1891 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.40 % Allowed : 18.80 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.18 (0.30), residues: 760 helix: 1.83 (0.32), residues: 285 sheet: -0.06 (0.50), residues: 109 loop : -1.82 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 409 HIS 0.004 0.001 HIS A 385 PHE 0.011 0.001 PHE A 371 TYR 0.015 0.002 TYR B 45 ARG 0.004 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 86 time to evaluate : 0.724 Fit side-chains REVERT: A 203 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7238 (mtm-85) REVERT: A 207 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6469 (tm-30) REVERT: A 338 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6529 (pp20) REVERT: A 366 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: B 82 ARG cc_start: 0.7580 (mmm160) cc_final: 0.7379 (mmm160) REVERT: B 216 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7869 (ttt180) REVERT: B 377 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7891 (tm-30) outliers start: 48 outliers final: 38 residues processed: 122 average time/residue: 0.2126 time to fit residues: 34.2591 Evaluate side-chains 122 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 81 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7733 Z= 0.216 Angle : 0.517 7.053 10770 Z= 0.258 Chirality : 0.037 0.169 1235 Planarity : 0.004 0.034 1178 Dihedral : 18.827 174.601 1891 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.63 % Allowed : 20.49 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.09 (0.30), residues: 760 helix: 1.86 (0.31), residues: 285 sheet: 0.14 (0.50), residues: 110 loop : -1.79 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.004 0.001 HIS A 495 PHE 0.011 0.001 PHE A 371 TYR 0.019 0.002 TYR B 153 ARG 0.003 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 82 time to evaluate : 0.758 Fit side-chains REVERT: A 203 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7247 (mtm-85) REVERT: A 207 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6450 (tm-30) REVERT: A 338 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6423 (pp20) REVERT: A 366 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: B 83 SER cc_start: 0.8443 (t) cc_final: 0.8184 (t) REVERT: B 153 TYR cc_start: 0.6610 (m-80) cc_final: 0.6408 (m-80) REVERT: B 216 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7888 (ttt180) REVERT: B 377 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7830 (tm-30) outliers start: 43 outliers final: 34 residues processed: 113 average time/residue: 0.2030 time to fit residues: 30.6817 Evaluate side-chains 115 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.1980 chunk 45 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7733 Z= 0.136 Angle : 0.471 7.225 10770 Z= 0.233 Chirality : 0.035 0.161 1235 Planarity : 0.003 0.034 1178 Dihedral : 18.705 174.209 1891 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.39 % Allowed : 24.04 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.26 (0.30), residues: 760 helix: 2.11 (0.32), residues: 286 sheet: 0.72 (0.52), residues: 99 loop : -1.63 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 409 HIS 0.002 0.001 HIS A 495 PHE 0.008 0.001 PHE A 371 TYR 0.011 0.001 TYR A 229 ARG 0.003 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7546 (mtt180) cc_final: 0.7197 (mtm-85) REVERT: A 207 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6392 (tm-30) REVERT: A 352 GLU cc_start: 0.8024 (tt0) cc_final: 0.7782 (tt0) REVERT: B 207 GLU cc_start: 0.8206 (tt0) cc_final: 0.7762 (tm-30) REVERT: B 436 MET cc_start: 0.7534 (mpp) cc_final: 0.7300 (mmm) outliers start: 22 outliers final: 16 residues processed: 108 average time/residue: 0.2104 time to fit residues: 30.0473 Evaluate side-chains 98 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.0270 chunk 39 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7733 Z= 0.165 Angle : 0.494 6.671 10770 Z= 0.248 Chirality : 0.036 0.161 1235 Planarity : 0.003 0.031 1178 Dihedral : 18.660 173.823 1891 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.70 % Allowed : 23.42 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.42 (0.30), residues: 760 helix: 2.24 (0.31), residues: 286 sheet: 0.78 (0.51), residues: 99 loop : -1.53 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS A 385 PHE 0.011 0.001 PHE A 371 TYR 0.012 0.001 TYR A 329 ARG 0.007 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7508 (mtt180) cc_final: 0.7163 (mtm-85) REVERT: A 207 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6380 (tm-30) REVERT: A 338 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6750 (pp20) REVERT: B 203 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7489 (mtm-85) REVERT: B 207 GLU cc_start: 0.8191 (tt0) cc_final: 0.7782 (tm-30) outliers start: 24 outliers final: 18 residues processed: 99 average time/residue: 0.2187 time to fit residues: 28.6128 Evaluate side-chains 96 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7733 Z= 0.159 Angle : 0.490 6.682 10770 Z= 0.244 Chirality : 0.036 0.161 1235 Planarity : 0.003 0.032 1178 Dihedral : 18.622 173.728 1891 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.54 % Allowed : 24.04 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.51 (0.30), residues: 760 helix: 2.30 (0.31), residues: 286 sheet: 0.79 (0.51), residues: 100 loop : -1.47 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS B 240 PHE 0.011 0.001 PHE A 371 TYR 0.023 0.001 TYR B 153 ARG 0.006 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7147 (mtm-85) REVERT: A 207 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 227 ARG cc_start: 0.7231 (mpp-170) cc_final: 0.6984 (mpp-170) REVERT: A 252 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7784 (mtm-85) REVERT: A 296 LEU cc_start: 0.8289 (tp) cc_final: 0.7846 (tp) REVERT: A 338 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6689 (pp20) REVERT: A 366 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 207 GLU cc_start: 0.8158 (tt0) cc_final: 0.7736 (tm-30) REVERT: B 436 MET cc_start: 0.7512 (mpp) cc_final: 0.7275 (mmm) outliers start: 23 outliers final: 20 residues processed: 98 average time/residue: 0.2172 time to fit residues: 28.5110 Evaluate side-chains 96 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7733 Z= 0.183 Angle : 0.506 7.599 10770 Z= 0.252 Chirality : 0.037 0.162 1235 Planarity : 0.003 0.031 1178 Dihedral : 18.630 173.538 1891 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.31 % Allowed : 22.65 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.52 (0.31), residues: 760 helix: 2.36 (0.31), residues: 285 sheet: 0.37 (0.50), residues: 110 loop : -1.38 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS A 385 PHE 0.015 0.001 PHE B 308 TYR 0.016 0.001 TYR A 284 ARG 0.005 0.000 ARG B 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7125 (mtm-85) REVERT: A 207 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6386 (tm-30) REVERT: A 227 ARG cc_start: 0.7252 (mpp-170) cc_final: 0.7037 (mpp-170) REVERT: A 252 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7817 (mtm-85) REVERT: A 296 LEU cc_start: 0.8302 (tp) cc_final: 0.7870 (tp) REVERT: A 338 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6670 (pp20) REVERT: A 366 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7363 (tm-30) REVERT: B 153 TYR cc_start: 0.6273 (m-80) cc_final: 0.5884 (m-80) REVERT: B 207 GLU cc_start: 0.8246 (tt0) cc_final: 0.7861 (tm-30) outliers start: 28 outliers final: 27 residues processed: 100 average time/residue: 0.2145 time to fit residues: 28.9941 Evaluate side-chains 103 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142028 restraints weight = 9087.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144926 restraints weight = 5025.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146688 restraints weight = 3393.511| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7733 Z= 0.133 Angle : 0.478 7.514 10770 Z= 0.237 Chirality : 0.035 0.161 1235 Planarity : 0.003 0.032 1178 Dihedral : 18.567 173.470 1891 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.85 % Allowed : 23.11 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.71 (0.31), residues: 760 helix: 2.48 (0.31), residues: 286 sheet: 0.88 (0.51), residues: 101 loop : -1.35 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 409 HIS 0.003 0.000 HIS B 347 PHE 0.010 0.001 PHE B 308 TYR 0.020 0.001 TYR A 284 ARG 0.005 0.000 ARG B 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.25 seconds wall clock time: 30 minutes 3.04 seconds (1803.04 seconds total)