Starting phenix.real_space_refine on Sat Apr 6 21:36:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/04_2024/6ukt_20812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/04_2024/6ukt_20812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/04_2024/6ukt_20812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/04_2024/6ukt_20812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/04_2024/6ukt_20812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/04_2024/6ukt_20812_updated.pdb" } resolution = 3.87 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= 0.615 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 2 5.49 5 S 46 5.16 5 C 5613 2.51 5 N 1596 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3834 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 23, 'TRANS': 459} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2128 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 4, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 770 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "D" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 753 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 595 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 204 Time building chain proxies: 5.56, per 1000 atoms: 0.62 Number of scatterers: 8979 At special positions: 0 Unit cell: (134.62, 125.08, 90.1, 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 46 16.00 P 2 15.00 O 1722 8.00 N 1596 7.00 C 5613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 30.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.807A pdb=" N GLU A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 80 through 83 No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 86 through 96 Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 111 through 127 removed outlier: 4.063A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.585A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 removed outlier: 4.603A pdb=" N VAL A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 241 through 258 Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 385 through 398 removed outlier: 5.095A pdb=" N VAL A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 477 through 480 removed outlier: 3.561A pdb=" N MET A 480 " --> pdb=" O HIS A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 104 through 107 No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 121 through 132 removed outlier: 3.982A pdb=" N GLY B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.910A pdb=" N ASP B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'B' and resid 220 through 222 removed outlier: 6.396A pdb=" N SER B 263 " --> pdb=" O ILE B 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 92 through 97 removed outlier: 3.601A pdb=" N ASN C 96 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET C 34 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 51 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 18 through 22 Processing sheet with id= D, first strand: chain 'D' and resid 92 through 98 removed outlier: 3.580A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE D 51 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA D 40 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG D 45 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 35 through 39 Processing sheet with id= F, first strand: chain 'F' and resid 20 through 23 Processing sheet with id= G, first strand: chain 'F' and resid 34 through 36 245 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 3.82 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: 2953 1.34 - 1.45: 1450 1.45 - 1.57: 4648 1.57 - 1.69: 7 1.69 - 1.81: 68 Bond restraints: 9126 Sorted by residual: bond pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O1P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O2P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C ASP A 439 " pdb=" N TPO A 440 " ideal model delta sigma weight residual 1.329 1.292 0.037 1.40e-02 5.10e+03 7.17e+00 bond pdb=" CB ARG A 219 " pdb=" CG ARG A 219 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.34e+00 ... (remaining 9121 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.06: 131 105.06 - 112.30: 4477 112.30 - 119.53: 3135 119.53 - 126.77: 4523 126.77 - 134.01: 103 Bond angle restraints: 12369 Sorted by residual: angle pdb=" N MET A 467 " pdb=" CA MET A 467 " pdb=" C MET A 467 " ideal model delta sigma weight residual 111.07 117.41 -6.34 1.07e+00 8.73e-01 3.51e+01 angle pdb=" C SER A 402 " pdb=" N VAL A 403 " pdb=" CA VAL A 403 " ideal model delta sigma weight residual 120.24 123.20 -2.96 6.30e-01 2.52e+00 2.21e+01 angle pdb=" N ASN A 453 " pdb=" CA ASN A 453 " pdb=" C ASN A 453 " ideal model delta sigma weight residual 109.81 119.82 -10.01 2.21e+00 2.05e-01 2.05e+01 angle pdb=" C GLU A 444 " pdb=" N TYR A 445 " pdb=" CA TYR A 445 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" N LYS A 462 " pdb=" CA LYS A 462 " pdb=" C LYS A 462 " ideal model delta sigma weight residual 109.81 118.98 -9.17 2.21e+00 2.05e-01 1.72e+01 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4646 17.02 - 34.03: 654 34.03 - 51.05: 144 51.05 - 68.07: 21 68.07 - 85.09: 18 Dihedral angle restraints: 5483 sinusoidal: 2012 harmonic: 3471 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 164.34 -71.34 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual 93.00 32.43 60.57 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CA LYS A 462 " pdb=" C LYS A 462 " pdb=" N PRO A 463 " pdb=" CA PRO A 463 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 5480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1175 0.076 - 0.151: 203 0.151 - 0.227: 22 0.227 - 0.302: 5 0.302 - 0.378: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CB ILE A 211 " pdb=" CA ILE A 211 " pdb=" CG1 ILE A 211 " pdb=" CG2 ILE A 211 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB VAL A 330 " pdb=" CA VAL A 330 " pdb=" CG1 VAL A 330 " pdb=" CG2 VAL A 330 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASN A 453 " pdb=" N ASN A 453 " pdb=" C ASN A 453 " pdb=" CB ASN A 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1403 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 374 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" CG ASN A 374 " 0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 374 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN A 374 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 357 " -0.056 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO A 358 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 87 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO D 88 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.038 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2131 2.78 - 3.31: 8667 3.31 - 3.84: 14587 3.84 - 4.37: 15247 4.37 - 4.90: 25078 Nonbonded interactions: 65710 Sorted by model distance: nonbonded pdb=" O SER A 335 " pdb=" OG1 THR A 338 " model vdw 2.247 2.440 nonbonded pdb=" O PRO A 213 " pdb=" OG1 THR A 217 " model vdw 2.256 2.440 nonbonded pdb=" O ASN A 26 " pdb=" OG SER A 30 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR C 97 " pdb=" O VAL C 100 " model vdw 2.279 2.440 nonbonded pdb=" O GLU A 15 " pdb=" OG1 THR A 19 " model vdw 2.284 2.440 ... (remaining 65705 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: 0.730 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: 2.860 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.440 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.007 0.110 9126 Z= 0.454 Angle : 1.034 10.524 12369 Z= 0.565 Chirality : 0.058 0.378 1406 Planarity : 0.007 0.083 1623 Dihedral : 16.893 85.086 3232 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % Rotamer: Outliers : 0.46 % Allowed : 13.30 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.19), residues: 1174 helix: -2.62 (0.19), residues: 385 sheet: -3.87 (0.37), residues: 120 loop : -3.85 (0.19), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 114 HIS 0.006 0.002 HIS E 96 PHE 0.029 0.003 PHE E 98 TYR 0.039 0.002 TYR E 107 ARG 0.034 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ASP cc_start: 0.8022 (t0) cc_final: 0.7811 (t0) outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.3755 time to fit residues: 48.7798 Evaluate side-chains 80 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 108 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 229 ASN A 273 HIS ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN A 477 HIS B 172 GLN B 204 GLN B 241 ASN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9126 Z= 0.170 Angle : 0.625 7.696 12369 Z= 0.331 Chirality : 0.040 0.172 1406 Planarity : 0.005 0.074 1623 Dihedral : 6.127 32.249 1304 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.44 % Favored : 87.48 % Rotamer: Outliers : 1.15 % Allowed : 20.41 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.21), residues: 1174 helix: -1.08 (0.24), residues: 396 sheet: -3.76 (0.37), residues: 120 loop : -3.59 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 114 HIS 0.002 0.001 HIS A 62 PHE 0.030 0.001 PHE B 336 TYR 0.014 0.001 TYR A 445 ARG 0.004 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8572 (t0) REVERT: A 233 ASP cc_start: 0.7689 (t0) cc_final: 0.7488 (t0) REVERT: A 439 ASP cc_start: 0.7752 (t0) cc_final: 0.7539 (t0) REVERT: B 208 ARG cc_start: 0.7811 (tpp80) cc_final: 0.7605 (ttm-80) outliers start: 10 outliers final: 3 residues processed: 100 average time/residue: 0.3774 time to fit residues: 46.7934 Evaluate side-chains 81 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 0.0050 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN B 304 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9126 Z= 0.211 Angle : 0.629 7.639 12369 Z= 0.331 Chirality : 0.040 0.200 1406 Planarity : 0.005 0.068 1623 Dihedral : 5.869 37.321 1302 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.48 % Favored : 85.43 % Rotamer: Outliers : 1.95 % Allowed : 23.17 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.22), residues: 1174 helix: -0.52 (0.25), residues: 405 sheet: -3.76 (0.35), residues: 122 loop : -3.48 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 114 HIS 0.003 0.001 HIS A 158 PHE 0.019 0.002 PHE B 336 TYR 0.014 0.001 TYR C 37 ARG 0.005 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7754 (t0) cc_final: 0.7500 (t0) REVERT: A 439 ASP cc_start: 0.7852 (t0) cc_final: 0.7608 (t0) REVERT: B 208 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7548 (ttm-80) REVERT: C 81 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7052 (mm110) REVERT: D 3 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7864 (mp10) outliers start: 17 outliers final: 5 residues processed: 100 average time/residue: 0.3470 time to fit residues: 43.7705 Evaluate side-chains 82 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 51 optimal weight: 20.0000 chunk 72 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9126 Z= 0.164 Angle : 0.599 7.183 12369 Z= 0.312 Chirality : 0.040 0.148 1406 Planarity : 0.004 0.068 1623 Dihedral : 5.538 38.590 1302 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 2.18 % Allowed : 24.31 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.23), residues: 1174 helix: -0.12 (0.26), residues: 402 sheet: -3.26 (0.37), residues: 125 loop : -3.37 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 114 HIS 0.002 0.000 HIS A 62 PHE 0.010 0.001 PHE B 354 TYR 0.013 0.001 TYR A 445 ARG 0.010 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7668 (t0) cc_final: 0.7375 (t0) REVERT: A 325 ARG cc_start: 0.7344 (mtp180) cc_final: 0.7136 (mtp180) REVERT: A 439 ASP cc_start: 0.7728 (t0) cc_final: 0.7474 (t0) REVERT: B 190 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8735 (t) REVERT: B 204 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: B 208 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7499 (ttm-80) REVERT: B 345 LYS cc_start: 0.9019 (tppp) cc_final: 0.8650 (tppp) REVERT: E 82 MET cc_start: 0.5829 (mmm) cc_final: 0.5439 (mmt) outliers start: 19 outliers final: 7 residues processed: 97 average time/residue: 0.3453 time to fit residues: 42.3920 Evaluate side-chains 84 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 0.0170 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9126 Z= 0.233 Angle : 0.629 6.828 12369 Z= 0.330 Chirality : 0.042 0.378 1406 Planarity : 0.004 0.065 1623 Dihedral : 5.700 40.592 1302 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 1.83 % Allowed : 26.26 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.23), residues: 1174 helix: 0.06 (0.26), residues: 402 sheet: -3.51 (0.38), residues: 110 loop : -3.32 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 114 HIS 0.003 0.001 HIS A 158 PHE 0.012 0.002 PHE B 336 TYR 0.018 0.001 TYR A 412 ARG 0.005 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7763 (t0) cc_final: 0.7438 (t0) REVERT: A 380 MET cc_start: 0.8273 (ttm) cc_final: 0.7895 (ttp) REVERT: A 439 ASP cc_start: 0.7754 (t0) cc_final: 0.7497 (t0) REVERT: A 470 MET cc_start: 0.7600 (tpp) cc_final: 0.7237 (tpp) REVERT: B 190 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8813 (t) REVERT: B 208 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7657 (ttm-80) REVERT: B 345 LYS cc_start: 0.9082 (tppp) cc_final: 0.8696 (tppp) REVERT: E 82 MET cc_start: 0.5734 (mmm) cc_final: 0.4887 (mmm) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.3381 time to fit residues: 38.4066 Evaluate side-chains 84 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9126 Z= 0.241 Angle : 0.648 10.480 12369 Z= 0.336 Chirality : 0.042 0.334 1406 Planarity : 0.004 0.065 1623 Dihedral : 5.732 38.476 1302 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 2.41 % Allowed : 27.52 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.23), residues: 1174 helix: 0.20 (0.26), residues: 399 sheet: -3.42 (0.38), residues: 111 loop : -3.28 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 114 HIS 0.004 0.001 HIS A 324 PHE 0.016 0.002 PHE E 37 TYR 0.022 0.001 TYR A 412 ARG 0.006 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7819 (t0) cc_final: 0.7488 (t0) REVERT: A 343 MET cc_start: 0.8668 (mmm) cc_final: 0.8396 (mmm) REVERT: A 380 MET cc_start: 0.8234 (ttm) cc_final: 0.8021 (ttp) REVERT: A 439 ASP cc_start: 0.7755 (t0) cc_final: 0.7468 (t0) REVERT: A 470 MET cc_start: 0.7717 (tpp) cc_final: 0.7517 (tpp) REVERT: B 190 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8848 (t) REVERT: E 82 MET cc_start: 0.5658 (mmm) cc_final: 0.4917 (mmm) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 0.3585 time to fit residues: 44.8453 Evaluate side-chains 92 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9126 Z= 0.181 Angle : 0.616 10.686 12369 Z= 0.318 Chirality : 0.041 0.306 1406 Planarity : 0.004 0.065 1623 Dihedral : 5.453 38.670 1302 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 2.18 % Allowed : 28.90 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.24), residues: 1174 helix: 0.30 (0.27), residues: 400 sheet: -3.13 (0.39), residues: 121 loop : -3.26 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 114 HIS 0.002 0.001 HIS A 62 PHE 0.015 0.001 PHE B 336 TYR 0.021 0.001 TYR A 412 ARG 0.007 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7680 (t0) cc_final: 0.7341 (t0) REVERT: A 343 MET cc_start: 0.8777 (mmm) cc_final: 0.8416 (mmm) REVERT: A 439 ASP cc_start: 0.7679 (t0) cc_final: 0.7376 (t0) REVERT: B 43 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7437 (pp20) REVERT: B 190 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8773 (t) REVERT: B 214 CYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8052 (t) REVERT: E 82 MET cc_start: 0.5675 (mmm) cc_final: 0.4683 (mmm) outliers start: 19 outliers final: 10 residues processed: 98 average time/residue: 0.3443 time to fit residues: 42.5437 Evaluate side-chains 90 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 0.0770 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 0.0470 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9126 Z= 0.154 Angle : 0.606 10.735 12369 Z= 0.308 Chirality : 0.040 0.288 1406 Planarity : 0.004 0.066 1623 Dihedral : 5.061 39.000 1302 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 1.95 % Allowed : 29.70 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.24), residues: 1174 helix: 0.46 (0.27), residues: 400 sheet: -2.77 (0.38), residues: 128 loop : -3.20 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 114 HIS 0.002 0.000 HIS A 62 PHE 0.017 0.001 PHE B 336 TYR 0.023 0.001 TYR A 412 ARG 0.007 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7565 (t0) cc_final: 0.7241 (t0) REVERT: A 306 MET cc_start: 0.7963 (mmm) cc_final: 0.7194 (mmm) REVERT: A 343 MET cc_start: 0.8772 (mmm) cc_final: 0.8422 (mmm) REVERT: A 439 ASP cc_start: 0.7645 (t0) cc_final: 0.7350 (t0) REVERT: B 43 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6442 (pp20) REVERT: B 204 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: B 208 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7620 (ttm-80) REVERT: E 82 MET cc_start: 0.5655 (mmm) cc_final: 0.4665 (mmm) outliers start: 17 outliers final: 9 residues processed: 110 average time/residue: 0.3476 time to fit residues: 47.9833 Evaluate side-chains 92 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 64 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 overall best weight: 2.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9126 Z= 0.236 Angle : 0.660 9.302 12369 Z= 0.341 Chirality : 0.042 0.271 1406 Planarity : 0.005 0.099 1623 Dihedral : 5.376 38.454 1302 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.71 % Favored : 86.20 % Rotamer: Outliers : 1.72 % Allowed : 30.39 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.24), residues: 1174 helix: 0.41 (0.27), residues: 400 sheet: -2.94 (0.42), residues: 111 loop : -3.18 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 114 HIS 0.003 0.001 HIS E 96 PHE 0.017 0.002 PHE B 336 TYR 0.029 0.001 TYR A 412 ARG 0.011 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7694 (t0) cc_final: 0.7324 (t0) REVERT: A 306 MET cc_start: 0.8192 (mmm) cc_final: 0.7960 (mmm) REVERT: A 343 MET cc_start: 0.8908 (mmm) cc_final: 0.8669 (mmm) REVERT: A 439 ASP cc_start: 0.7690 (t0) cc_final: 0.7392 (t0) REVERT: B 43 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: B 208 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7679 (ttm-80) REVERT: B 214 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8037 (t) REVERT: E 82 MET cc_start: 0.5259 (mmm) cc_final: 0.4732 (mmm) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.3486 time to fit residues: 42.4662 Evaluate side-chains 91 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9126 Z= 0.182 Angle : 0.628 9.912 12369 Z= 0.324 Chirality : 0.042 0.274 1406 Planarity : 0.005 0.088 1623 Dihedral : 5.235 37.518 1302 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.12 % Favored : 86.88 % Rotamer: Outliers : 1.61 % Allowed : 30.16 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.24), residues: 1174 helix: 0.35 (0.27), residues: 400 sheet: -2.78 (0.39), residues: 135 loop : -3.18 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.001 HIS A 324 PHE 0.023 0.001 PHE B 354 TYR 0.022 0.001 TYR D 94 ARG 0.012 0.001 ARG A 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7604 (t0) cc_final: 0.7262 (t0) REVERT: A 306 MET cc_start: 0.8118 (mmm) cc_final: 0.7406 (mmm) REVERT: A 343 MET cc_start: 0.8881 (mmm) cc_final: 0.8644 (mmm) REVERT: A 439 ASP cc_start: 0.7645 (t0) cc_final: 0.7351 (t0) REVERT: B 43 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: B 171 GLN cc_start: 0.8595 (tp-100) cc_final: 0.7268 (pm20) REVERT: B 214 CYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8198 (t) REVERT: B 349 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8516 (pttm) REVERT: E 82 MET cc_start: 0.5702 (mmm) cc_final: 0.5165 (mmm) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.3427 time to fit residues: 40.7905 Evaluate side-chains 87 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.0020 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** 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 = 0.3278 r_free = 0.3278 target = 0.060544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050964 restraints weight = 54447.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052235 restraints weight = 34271.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053136 restraints weight = 24933.626| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9126 Z= 0.155 Angle : 0.616 10.254 12369 Z= 0.316 Chirality : 0.041 0.273 1406 Planarity : 0.005 0.095 1623 Dihedral : 4.945 36.651 1302 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 1.49 % Allowed : 30.39 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.24), residues: 1174 helix: 0.48 (0.27), residues: 399 sheet: -2.54 (0.40), residues: 135 loop : -3.10 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 258 HIS 0.002 0.000 HIS A 62 PHE 0.018 0.001 PHE B 336 TYR 0.021 0.001 TYR A 412 ARG 0.021 0.001 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.91 seconds wall clock time: 35 minutes 46.28 seconds (2146.28 seconds total)