Starting phenix.real_space_refine on Fri Dec 8 19:05:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/12_2023/6ukt_20812_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/12_2023/6ukt_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_20812/12_2023/6ukt_20812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/12_2023/6ukt_20812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/12_2023/6ukt_20812_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ukt_20812/12_2023/6ukt_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-1.21rc1-5172/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: 5.07, per 1000 atoms: 0.56 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: 3.33 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: 1.60 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: 1.95 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: 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: 0.650 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: 2.890 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.570 Find NCS groups from input model: 0.270 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- 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 : 1.110 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 outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.3713 time to fit residues: 48.2457 Evaluate side-chains 80 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0781 time to fit residues: 1.4035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1455 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 : 0.627 7.639 12369 Z= 0.332 Chirality : 0.040 0.169 1406 Planarity : 0.005 0.074 1623 Dihedral : 6.123 32.481 1302 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.52 % Favored : 87.39 % Rotamer: Outliers : 0.92 % Allowed : 20.64 % 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: -4.03 (0.21), residues: 1174 helix: -1.13 (0.24), residues: 402 sheet: -3.74 (0.37), residues: 120 loop : -3.65 (0.21), residues: 652 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 0.029 0.001 PHE B 336 TYR 0.014 0.001 TYR A 445 ARG 0.004 0.000 ARG A 43 *********************** 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 99 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 98 average time/residue: 0.3737 time to fit residues: 45.2484 Evaluate side-chains 79 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0957 time to fit residues: 1.7234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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** B 304 GLN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9126 Z= 0.161 Angle : 0.591 7.786 12369 Z= 0.310 Chirality : 0.039 0.182 1406 Planarity : 0.004 0.069 1623 Dihedral : 5.535 38.156 1302 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 2.06 % Allowed : 22.48 % Favored : 75.46 % 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: -3.47 (0.23), residues: 1174 helix: -0.45 (0.25), residues: 404 sheet: -3.44 (0.37), residues: 125 loop : -3.47 (0.21), residues: 645 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 0.020 0.001 PHE B 336 TYR 0.013 0.001 TYR A 445 ARG 0.005 0.000 ARG A 75 *********************** 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 107 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.107 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 outliers start: 18 outliers final: 5 residues processed: 103 average time/residue: 0.3297 time to fit residues: 43.0490 Evaluate side-chains 83 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0907 time to fit residues: 2.2259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- 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 3 GLN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9126 Z= 0.210 Angle : 0.624 8.091 12369 Z= 0.326 Chirality : 0.041 0.421 1406 Planarity : 0.005 0.067 1623 Dihedral : 5.546 40.463 1302 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.29 % Favored : 86.63 % Rotamer: Outliers : 1.38 % Allowed : 24.31 % Favored : 74.31 % 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: -3.16 (0.23), residues: 1174 helix: -0.07 (0.26), residues: 401 sheet: -3.39 (0.38), residues: 120 loop : -3.33 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 114 HIS 0.003 0.001 HIS A 158 PHE 0.011 0.001 PHE B 354 TYR 0.013 0.001 TYR A 445 ARG 0.011 0.001 ARG C 75 *********************** 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 91 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.088 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 outliers start: 12 outliers final: 6 residues processed: 88 average time/residue: 0.3733 time to fit residues: 41.0520 Evaluate side-chains 79 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1093 time to fit residues: 2.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 98 optimal weight: 0.0000 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9126 Z= 0.183 Angle : 0.596 6.397 12369 Z= 0.312 Chirality : 0.041 0.346 1406 Planarity : 0.004 0.065 1623 Dihedral : 5.421 41.246 1302 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 1.03 % Allowed : 25.46 % 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: -2.97 (0.24), residues: 1174 helix: 0.12 (0.26), residues: 402 sheet: -3.24 (0.39), residues: 120 loop : -3.25 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 114 HIS 0.004 0.001 HIS A 324 PHE 0.013 0.001 PHE B 336 TYR 0.022 0.001 TYR A 412 ARG 0.008 0.001 ARG A 143 *********************** 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 88 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 1.017 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 outliers start: 9 outliers final: 3 residues processed: 87 average time/residue: 0.3561 time to fit residues: 38.9737 Evaluate side-chains 79 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0894 time to fit residues: 1.9042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 0.0040 chunk 28 optimal weight: 0.0370 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.3668 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.2780 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= 0.142 Angle : 0.590 12.175 12369 Z= 0.299 Chirality : 0.040 0.315 1406 Planarity : 0.004 0.067 1623 Dihedral : 4.979 40.936 1302 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.26 % Allowed : 25.80 % Favored : 72.94 % 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: -2.76 (0.24), residues: 1174 helix: 0.32 (0.27), residues: 402 sheet: -2.78 (0.39), residues: 127 loop : -3.23 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 131 HIS 0.003 0.001 HIS A 324 PHE 0.011 0.001 PHE E 98 TYR 0.026 0.001 TYR A 412 ARG 0.007 0.000 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 103 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.042 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 outliers start: 11 outliers final: 3 residues processed: 98 average time/residue: 0.3627 time to fit residues: 44.3343 Evaluate side-chains 81 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0931 time to fit residues: 1.8188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 84 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.0270 overall best weight: 1.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9126 Z= 0.184 Angle : 0.615 10.178 12369 Z= 0.315 Chirality : 0.041 0.280 1406 Planarity : 0.005 0.092 1623 Dihedral : 5.086 42.817 1302 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 0.69 % Allowed : 27.29 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.24), residues: 1174 helix: 0.41 (0.27), residues: 401 sheet: -2.99 (0.42), residues: 110 loop : -3.18 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 114 HIS 0.002 0.001 HIS A 158 PHE 0.016 0.001 PHE B 336 TYR 0.014 0.001 TYR E 110 ARG 0.013 0.001 ARG C 75 *********************** 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 89 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 89 average time/residue: 0.3775 time to fit residues: 41.8778 Evaluate side-chains 79 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0952 time to fit residues: 1.5620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 0.0170 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.0570 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 1.3538 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9126 Z= 0.178 Angle : 0.621 9.998 12369 Z= 0.316 Chirality : 0.041 0.270 1406 Planarity : 0.004 0.074 1623 Dihedral : 5.086 42.872 1302 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.57 % Allowed : 28.44 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.24), residues: 1174 helix: 0.43 (0.27), residues: 402 sheet: -2.74 (0.40), residues: 123 loop : -3.13 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 114 HIS 0.002 0.001 HIS A 62 PHE 0.017 0.001 PHE B 336 TYR 0.015 0.001 TYR A 412 ARG 0.007 0.000 ARG D 45 *********************** 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 88 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 86 average time/residue: 0.3640 time to fit residues: 39.2145 Evaluate side-chains 81 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0935 time to fit residues: 1.6919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7967 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9126 Z= 0.170 Angle : 0.618 10.036 12369 Z= 0.315 Chirality : 0.041 0.260 1406 Planarity : 0.005 0.094 1623 Dihedral : 5.005 42.536 1302 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 0.57 % Allowed : 28.78 % Favored : 70.64 % 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: -2.50 (0.24), residues: 1174 helix: 0.51 (0.27), residues: 402 sheet: -2.60 (0.41), residues: 128 loop : -3.06 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.002 0.001 HIS A 90 PHE 0.018 0.001 PHE B 336 TYR 0.016 0.001 TYR A 412 ARG 0.008 0.000 ARG A 458 *********************** 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 88 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.113 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 outliers start: 5 outliers final: 1 residues processed: 86 average time/residue: 0.3487 time to fit residues: 38.0184 Evaluate side-chains 80 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5389 time to fit residues: 2.0418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 74 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 overall best weight: 0.7822 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9126 Z= 0.166 Angle : 0.632 10.971 12369 Z= 0.317 Chirality : 0.041 0.259 1406 Planarity : 0.005 0.092 1623 Dihedral : 4.838 42.326 1302 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 29.70 % Favored : 70.30 % 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: -2.39 (0.25), residues: 1174 helix: 0.55 (0.28), residues: 402 sheet: -2.37 (0.42), residues: 128 loop : -2.99 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 211 HIS 0.002 0.000 HIS A 62 PHE 0.019 0.001 PHE B 336 TYR 0.017 0.001 TYR A 412 ARG 0.009 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 86 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.164 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 outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.4496 time to fit residues: 49.2541 Evaluate side-chains 81 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 26 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049999 restraints weight = 55063.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.051440 restraints weight = 33151.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052435 restraints weight = 23453.164| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9126 Z= 0.185 Angle : 0.638 10.321 12369 Z= 0.321 Chirality : 0.041 0.257 1406 Planarity : 0.005 0.087 1623 Dihedral : 4.914 42.214 1302 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 0.23 % Allowed : 29.82 % Favored : 69.95 % 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: -2.30 (0.25), residues: 1174 helix: 0.62 (0.28), residues: 395 sheet: -2.35 (0.43), residues: 128 loop : -2.90 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 114 HIS 0.002 0.001 HIS A 158 PHE 0.026 0.001 PHE E 67 TYR 0.019 0.001 TYR A 412 ARG 0.008 0.001 ARG A 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1834.63 seconds wall clock time: 34 minutes 11.87 seconds (2051.87 seconds total)