Starting phenix.real_space_refine on Thu Feb 15 01:03:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v68_31738/02_2024/7v68_31738_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v68_31738/02_2024/7v68_31738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v68_31738/02_2024/7v68_31738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v68_31738/02_2024/7v68_31738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v68_31738/02_2024/7v68_31738_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v68_31738/02_2024/7v68_31738_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2117 atoms to isotropic. 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 S 66 5.16 5 Cl 1 4.86 5 C 5496 2.51 5 N 1451 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8577 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2197 Unusual residues: {'2CU': 1, 'IXO': 1} Classifications: {'peptide': 277, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 266, None: 2} Not linked: pdbres="GLN R 471 " pdbres="IXO R 501 " Not linked: pdbres="IXO R 501 " pdbres="2CU R 502 " Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.93, per 1000 atoms: 0.57 Number of scatterers: 8577 At special positions: 0 Unit cell: (94.2936, 122.027, 123.414, 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) Cl 1 17.00 S 66 16.00 O 1563 8.00 N 1451 7.00 C 5496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " 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=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 35.8% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.316A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.623A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.730A pdb=" N VAL A 332 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.515A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'R' and resid 30 through 59 Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 66 through 95 removed outlier: 4.555A pdb=" N PHE R 70 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER R 85 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N MET R 86 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN R 87 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU R 88 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE R 94 " --> pdb=" O VAL R 91 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS R 95 " --> pdb=" O TYR R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 135 Processing helix chain 'R' and resid 140 through 144 Processing helix chain 'R' and resid 147 through 175 Proline residue: R 166 - end of helix removed outlier: 5.018A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 191 No H-bonds generated for 'chain 'R' and resid 189 through 191' Processing helix chain 'R' and resid 193 through 222 removed outlier: 4.141A pdb=" N PHE R 197 " --> pdb=" O ALA R 194 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY R 198 " --> pdb=" O VAL R 195 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR R 199 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR R 205 " --> pdb=" O ALA R 202 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU R 206 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Proline residue: R 207 - end of helix Processing helix chain 'R' and resid 392 through 419 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 422 through 424 No H-bonds generated for 'chain 'R' and resid 422 through 424' Processing helix chain 'R' and resid 432 through 455 removed outlier: 4.058A pdb=" N SER R 436 " --> pdb=" O ASP R 432 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE R 437 " --> pdb=" O THR R 433 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY R 438 " --> pdb=" O VAL R 434 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 458 through 470 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.828A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 61 through 63 Processing sheet with id= C, first strand: chain 'B' and resid 111 through 115 removed outlier: 6.027A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.708A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 262 through 265 removed outlier: 3.662A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.024A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.523A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.541A pdb=" N PHE S 80 " --> pdb=" O SER S 71 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.543A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET S 34 " --> pdb=" O ILE S 51 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.595A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 214 through 218 removed outlier: 3.686A pdb=" N TYR S 163 " --> pdb=" O MET S 218 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 930 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: 2.42 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 5 1.20 - 1.35: 2720 1.35 - 1.51: 2564 1.51 - 1.66: 3377 1.66 - 1.82: 97 Bond restraints: 8763 Sorted by residual: bond pdb=" CG PRO R 181 " pdb=" CD PRO R 181 " ideal model delta sigma weight residual 1.503 1.042 0.461 3.40e-02 8.65e+02 1.83e+02 bond pdb=" C08 2CU R 502 " pdb=" N05 2CU R 502 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C05 IXO R 501 " pdb=" C06 IXO R 501 " ideal model delta sigma weight residual 1.450 1.564 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C18 2CU R 502 " pdb=" N19 2CU R 502 " ideal model delta sigma weight residual 1.356 1.466 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C24 2CU R 502 " pdb=" N26 2CU R 502 " ideal model delta sigma weight residual 1.353 1.463 -0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 59.91 - 83.92: 4 83.92 - 107.94: 322 107.94 - 131.95: 11567 131.95 - 155.97: 22 155.97 - 179.98: 2 Bond angle restraints: 11917 Sorted by residual: angle pdb=" N PRO R 181 " pdb=" CD PRO R 181 " pdb=" CG PRO R 181 " ideal model delta sigma weight residual 103.20 79.30 23.90 1.50e+00 4.44e-01 2.54e+02 angle pdb=" CA PRO R 181 " pdb=" CB PRO R 181 " pdb=" CG PRO R 181 " ideal model delta sigma weight residual 104.50 85.23 19.27 1.90e+00 2.77e-01 1.03e+02 angle pdb=" CA PRO R 181 " pdb=" N PRO R 181 " pdb=" CD PRO R 181 " ideal model delta sigma weight residual 112.00 99.00 13.00 1.40e+00 5.10e-01 8.62e+01 angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 109.81 129.23 -19.42 2.21e+00 2.05e-01 7.72e+01 angle pdb=" CA PRO R 137 " pdb=" N PRO R 137 " pdb=" CD PRO R 137 " ideal model delta sigma weight residual 112.00 103.74 8.26 1.40e+00 5.10e-01 3.48e+01 ... (remaining 11912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 4861 22.59 - 45.17: 260 45.17 - 67.76: 10 67.76 - 90.35: 8 90.35 - 112.94: 1 Dihedral angle restraints: 5140 sinusoidal: 1881 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 426 " pdb=" SG CYS R 426 " pdb=" SG CYS R 429 " pdb=" CB CYS R 429 " ideal model delta sinusoidal sigma weight residual -86.00 -134.56 48.56 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual 122.80 134.50 -11.70 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" C TYR S 223 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual -122.60 -134.18 11.58 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 5137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1377 0.140 - 0.281: 7 0.281 - 0.421: 1 0.421 - 0.562: 0 0.562 - 0.702: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL A 13 " pdb=" CA VAL A 13 " pdb=" CG1 VAL A 13 " pdb=" CG2 VAL A 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB THR B 164 " pdb=" CA THR B 164 " pdb=" OG1 THR B 164 " pdb=" CG2 THR B 164 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1383 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 2CU R 502 " 0.801 2.00e-02 2.50e+03 6.36e-01 6.06e+03 pdb=" C06 2CU R 502 " -0.695 2.00e-02 2.50e+03 pdb=" C08 2CU R 502 " -0.086 2.00e-02 2.50e+03 pdb=" C10 2CU R 502 " 0.746 2.00e-02 2.50e+03 pdb=" N05 2CU R 502 " 0.089 2.00e-02 2.50e+03 pdb=" O09 2CU R 502 " -0.854 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 180 " -0.083 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO R 181 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 136 " -0.060 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO R 137 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 137 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 137 " -0.047 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 261 2.70 - 3.25: 9123 3.25 - 3.80: 14000 3.80 - 4.35: 17630 4.35 - 4.90: 29186 Nonbonded interactions: 70200 Sorted by model distance: nonbonded pdb=" OH TYR B 59 " pdb=" OE1 GLN B 75 " model vdw 2.151 2.440 nonbonded pdb=" O ALA R 408 " pdb=" OG1 THR R 412 " model vdw 2.187 2.440 nonbonded pdb=" OG SER R 85 " pdb=" OD1 ASP R 112 " model vdw 2.205 2.440 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.268 2.520 nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 443 " model vdw 2.279 2.440 ... (remaining 70195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 1.950 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 0.461 8763 Z= 0.493 Angle : 0.834 23.900 11917 Z= 0.437 Chirality : 0.049 0.702 1386 Planarity : 0.018 0.636 1484 Dihedral : 12.843 112.936 3027 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.10 % 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: -0.44 (0.25), residues: 1104 helix: 1.30 (0.26), residues: 395 sheet: -0.91 (0.31), residues: 261 loop : -1.31 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP R 435 HIS 0.009 0.001 HIS R 217 PHE 0.036 0.002 PHE B 253 TYR 0.026 0.002 TYR B 264 ARG 0.010 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 35 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7421 (mtmm) REVERT: A 251 ASP cc_start: 0.7115 (t70) cc_final: 0.6572 (t0) REVERT: A 270 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7409 (mtmm) REVERT: A 345 LYS cc_start: 0.8076 (tptt) cc_final: 0.7613 (tptt) REVERT: A 347 ASN cc_start: 0.7334 (m-40) cc_final: 0.6825 (m-40) REVERT: B 175 GLN cc_start: 0.7638 (pp30) cc_final: 0.7227 (pp30) REVERT: B 176 GLN cc_start: 0.7915 (pt0) cc_final: 0.7482 (pt0) REVERT: B 187 VAL cc_start: 0.8095 (t) cc_final: 0.7541 (t) REVERT: B 188 MET cc_start: 0.6979 (mmt) cc_final: 0.6750 (mmt) REVERT: B 220 GLN cc_start: 0.5820 (mt0) cc_final: 0.5496 (mt0) REVERT: B 253 PHE cc_start: 0.7849 (m-10) cc_final: 0.7445 (m-80) REVERT: B 277 SER cc_start: 0.7818 (t) cc_final: 0.7471 (t) REVERT: C 15 LEU cc_start: 0.8011 (mt) cc_final: 0.7621 (mt) REVERT: C 20 LYS cc_start: 0.7695 (pttm) cc_final: 0.7490 (pttm) REVERT: S 78 THR cc_start: 0.7827 (p) cc_final: 0.7593 (p) REVERT: S 182 ASN cc_start: 0.6684 (m110) cc_final: 0.6445 (m110) REVERT: S 192 SER cc_start: 0.7622 (t) cc_final: 0.7348 (t) REVERT: R 54 MET cc_start: 0.6286 (ptp) cc_final: 0.6039 (ptp) REVERT: R 84 PHE cc_start: 0.6220 (m-80) cc_final: 0.5727 (m-80) REVERT: R 86 MET cc_start: 0.4847 (mmp) cc_final: 0.4551 (mmp) REVERT: R 111 LEU cc_start: 0.7683 (tt) cc_final: 0.7470 (tp) REVERT: R 131 TYR cc_start: 0.7977 (t80) cc_final: 0.7769 (t80) REVERT: R 173 PHE cc_start: 0.6520 (t80) cc_final: 0.6227 (t80) REVERT: R 187 ILE cc_start: 0.6825 (tp) cc_final: 0.6614 (tp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2146 time to fit residues: 90.1887 Evaluate side-chains 286 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0570 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 417 ASN ** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8763 Z= 0.221 Angle : 0.651 8.708 11917 Z= 0.337 Chirality : 0.044 0.264 1386 Planarity : 0.005 0.058 1484 Dihedral : 5.290 52.892 1226 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.13 % Allowed : 14.54 % Favored : 83.33 % 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: -0.54 (0.25), residues: 1104 helix: 1.08 (0.25), residues: 392 sheet: -0.83 (0.31), residues: 262 loop : -1.30 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 435 HIS 0.012 0.001 HIS A 188 PHE 0.016 0.002 PHE A 199 TYR 0.021 0.002 TYR S 216 ARG 0.006 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 303 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 35 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7324 (mtmm) REVERT: A 197 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7676 (mmtt) REVERT: A 251 ASP cc_start: 0.7177 (t70) cc_final: 0.6540 (t0) REVERT: A 271 LYS cc_start: 0.6573 (ptpp) cc_final: 0.6211 (ptpp) REVERT: A 274 PHE cc_start: 0.6614 (t80) cc_final: 0.6148 (t80) REVERT: A 330 LYS cc_start: 0.8319 (mppt) cc_final: 0.8111 (mppt) REVERT: A 345 LYS cc_start: 0.8049 (tptt) cc_final: 0.7839 (tptt) REVERT: A 346 ASN cc_start: 0.8122 (m110) cc_final: 0.7678 (m110) REVERT: A 347 ASN cc_start: 0.7453 (m-40) cc_final: 0.7085 (m-40) REVERT: B 45 MET cc_start: 0.7859 (mtm) cc_final: 0.7655 (mtp) REVERT: B 63 TRP cc_start: 0.7969 (m100) cc_final: 0.7583 (m100) REVERT: B 65 THR cc_start: 0.7843 (m) cc_final: 0.7591 (p) REVERT: B 70 LEU cc_start: 0.7715 (mt) cc_final: 0.7367 (mt) REVERT: B 101 MET cc_start: 0.7470 (mtp) cc_final: 0.7192 (mtm) REVERT: B 146 LEU cc_start: 0.7928 (mm) cc_final: 0.7724 (mt) REVERT: B 175 GLN cc_start: 0.7628 (pp30) cc_final: 0.7385 (pp30) REVERT: B 188 MET cc_start: 0.7034 (mmt) cc_final: 0.6803 (mmm) REVERT: B 237 ASN cc_start: 0.8044 (p0) cc_final: 0.7837 (p0) REVERT: B 239 ASN cc_start: 0.6654 (t0) cc_final: 0.6438 (t0) REVERT: B 246 ASP cc_start: 0.8166 (t0) cc_final: 0.7567 (t0) REVERT: B 277 SER cc_start: 0.8040 (t) cc_final: 0.7790 (t) REVERT: B 340 ASN cc_start: 0.7213 (t0) cc_final: 0.6980 (t0) REVERT: C 15 LEU cc_start: 0.8014 (mt) cc_final: 0.7623 (mt) REVERT: S 182 ASN cc_start: 0.6684 (m110) cc_final: 0.6412 (m110) REVERT: R 52 LEU cc_start: 0.7217 (mt) cc_final: 0.6982 (mt) REVERT: R 54 MET cc_start: 0.6061 (ptp) cc_final: 0.5801 (ptp) REVERT: R 84 PHE cc_start: 0.6411 (m-80) cc_final: 0.5939 (m-80) REVERT: R 111 LEU cc_start: 0.7660 (tt) cc_final: 0.7456 (tp) REVERT: R 121 MET cc_start: 0.7101 (mtt) cc_final: 0.6678 (mtt) REVERT: R 173 PHE cc_start: 0.6553 (t80) cc_final: 0.6304 (t80) REVERT: R 187 ILE cc_start: 0.6892 (tp) cc_final: 0.6682 (tp) REVERT: R 201 ILE cc_start: 0.8133 (mt) cc_final: 0.7889 (mt) outliers start: 19 outliers final: 15 residues processed: 309 average time/residue: 0.2336 time to fit residues: 97.6617 Evaluate side-chains 308 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 293 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 217 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8763 Z= 0.287 Angle : 0.647 8.688 11917 Z= 0.336 Chirality : 0.044 0.251 1386 Planarity : 0.005 0.050 1484 Dihedral : 5.190 50.446 1226 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.25 % Allowed : 17.79 % Favored : 77.96 % 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: -0.71 (0.24), residues: 1104 helix: 0.85 (0.26), residues: 392 sheet: -0.95 (0.31), residues: 259 loop : -1.29 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 164 HIS 0.027 0.002 HIS A 213 PHE 0.011 0.002 PHE B 235 TYR 0.023 0.002 TYR B 264 ARG 0.004 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 297 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 35 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7418 (mtmm) REVERT: A 197 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7457 (mmtt) REVERT: A 251 ASP cc_start: 0.7187 (t70) cc_final: 0.6561 (t0) REVERT: A 274 PHE cc_start: 0.6609 (t80) cc_final: 0.6130 (t80) REVERT: A 330 LYS cc_start: 0.8331 (mppt) cc_final: 0.8080 (mppt) REVERT: A 345 LYS cc_start: 0.8067 (tptt) cc_final: 0.7832 (tptt) REVERT: A 346 ASN cc_start: 0.8155 (m110) cc_final: 0.7677 (m110) REVERT: A 347 ASN cc_start: 0.7486 (m-40) cc_final: 0.7108 (m-40) REVERT: B 45 MET cc_start: 0.7910 (mtm) cc_final: 0.7681 (mtp) REVERT: B 65 THR cc_start: 0.7892 (m) cc_final: 0.7599 (p) REVERT: B 101 MET cc_start: 0.7461 (mtp) cc_final: 0.7197 (mtm) REVERT: B 175 GLN cc_start: 0.7647 (pp30) cc_final: 0.7369 (pp30) REVERT: B 237 ASN cc_start: 0.8080 (p0) cc_final: 0.7850 (p0) REVERT: B 239 ASN cc_start: 0.6824 (t0) cc_final: 0.6590 (t0) REVERT: B 246 ASP cc_start: 0.8184 (t0) cc_final: 0.7506 (t0) REVERT: B 277 SER cc_start: 0.8126 (t) cc_final: 0.7864 (t) REVERT: B 304 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7544 (ttp80) REVERT: C 15 LEU cc_start: 0.8057 (mt) cc_final: 0.7677 (mt) REVERT: R 52 LEU cc_start: 0.7247 (mt) cc_final: 0.7011 (mt) REVERT: R 54 MET cc_start: 0.6076 (ptp) cc_final: 0.5816 (ptp) REVERT: R 84 PHE cc_start: 0.6392 (m-80) cc_final: 0.5944 (m-80) REVERT: R 111 LEU cc_start: 0.7695 (tt) cc_final: 0.7494 (tp) REVERT: R 121 MET cc_start: 0.7031 (mtt) cc_final: 0.6685 (mtt) REVERT: R 173 PHE cc_start: 0.6631 (t80) cc_final: 0.6364 (t80) REVERT: R 183 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5743 (p0) REVERT: R 187 ILE cc_start: 0.7105 (tp) cc_final: 0.6891 (tp) REVERT: R 201 ILE cc_start: 0.8077 (mt) cc_final: 0.7839 (mt) outliers start: 38 outliers final: 28 residues processed: 311 average time/residue: 0.2151 time to fit residues: 90.4748 Evaluate side-chains 316 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 287 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8763 Z= 0.332 Angle : 0.657 8.316 11917 Z= 0.344 Chirality : 0.045 0.228 1386 Planarity : 0.005 0.051 1484 Dihedral : 5.274 45.534 1226 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.03 % Allowed : 20.81 % Favored : 74.16 % 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: -0.78 (0.24), residues: 1104 helix: 0.80 (0.26), residues: 391 sheet: -0.98 (0.30), residues: 268 loop : -1.33 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 63 HIS 0.008 0.002 HIS A 188 PHE 0.018 0.002 PHE B 235 TYR 0.021 0.002 TYR S 163 ARG 0.003 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 288 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 35 LYS cc_start: 0.7951 (mtmm) cc_final: 0.7504 (mtmm) REVERT: A 197 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7806 (mmtt) REVERT: A 198 MET cc_start: 0.6517 (ttm) cc_final: 0.6249 (ttm) REVERT: A 251 ASP cc_start: 0.7168 (t70) cc_final: 0.6584 (t0) REVERT: A 330 LYS cc_start: 0.8337 (mppt) cc_final: 0.8049 (mppt) REVERT: A 345 LYS cc_start: 0.8105 (tptt) cc_final: 0.7766 (tptt) REVERT: A 347 ASN cc_start: 0.7495 (m-40) cc_final: 0.7057 (m-40) REVERT: B 45 MET cc_start: 0.7975 (mtm) cc_final: 0.7689 (mtp) REVERT: B 65 THR cc_start: 0.7901 (m) cc_final: 0.7545 (p) REVERT: B 171 ILE cc_start: 0.7420 (mm) cc_final: 0.6827 (mt) REVERT: B 175 GLN cc_start: 0.7670 (pp30) cc_final: 0.7377 (pp30) REVERT: B 188 MET cc_start: 0.7002 (mmm) cc_final: 0.6620 (mmm) REVERT: B 237 ASN cc_start: 0.8080 (p0) cc_final: 0.7840 (p0) REVERT: B 246 ASP cc_start: 0.8253 (t0) cc_final: 0.7581 (t0) REVERT: B 339 TRP cc_start: 0.7566 (m100) cc_final: 0.7231 (m100) REVERT: C 15 LEU cc_start: 0.8089 (mt) cc_final: 0.7711 (mt) REVERT: S 190 ARG cc_start: 0.6660 (ptt-90) cc_final: 0.6453 (ptt-90) REVERT: S 216 TYR cc_start: 0.7499 (m-80) cc_final: 0.7211 (m-10) REVERT: R 52 LEU cc_start: 0.7265 (mt) cc_final: 0.7027 (mt) REVERT: R 54 MET cc_start: 0.6174 (ptp) cc_final: 0.5848 (ptp) REVERT: R 84 PHE cc_start: 0.6418 (m-80) cc_final: 0.5949 (m-80) REVERT: R 111 LEU cc_start: 0.7729 (tt) cc_final: 0.7490 (tp) REVERT: R 121 MET cc_start: 0.7036 (mtt) cc_final: 0.6731 (mtt) REVERT: R 173 PHE cc_start: 0.6751 (t80) cc_final: 0.6459 (t80) REVERT: R 183 ASN cc_start: 0.6297 (OUTLIER) cc_final: 0.5856 (p0) REVERT: R 187 ILE cc_start: 0.7165 (tp) cc_final: 0.6965 (tp) REVERT: R 201 ILE cc_start: 0.8078 (mt) cc_final: 0.7760 (mt) outliers start: 45 outliers final: 34 residues processed: 302 average time/residue: 0.2130 time to fit residues: 85.9104 Evaluate side-chains 313 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 278 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0470 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 132 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8763 Z= 0.215 Angle : 0.612 8.870 11917 Z= 0.317 Chirality : 0.043 0.197 1386 Planarity : 0.005 0.051 1484 Dihedral : 5.173 43.264 1226 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.92 % Allowed : 22.26 % Favored : 72.82 % 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: -0.68 (0.25), residues: 1104 helix: 0.88 (0.26), residues: 392 sheet: -0.99 (0.31), residues: 266 loop : -1.22 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.005 0.001 HIS B 311 PHE 0.015 0.001 PHE B 235 TYR 0.017 0.002 TYR B 264 ARG 0.006 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 280 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 35 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7484 (mtmm) REVERT: A 197 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7786 (mmmt) REVERT: A 198 MET cc_start: 0.6509 (ttm) cc_final: 0.6221 (ttm) REVERT: A 251 ASP cc_start: 0.7189 (t70) cc_final: 0.6551 (t0) REVERT: A 274 PHE cc_start: 0.6532 (t80) cc_final: 0.6044 (t80) REVERT: A 345 LYS cc_start: 0.8101 (tptt) cc_final: 0.7755 (tptt) REVERT: A 346 ASN cc_start: 0.8075 (m110) cc_final: 0.7670 (m110) REVERT: A 347 ASN cc_start: 0.7410 (m-40) cc_final: 0.6962 (m-40) REVERT: B 45 MET cc_start: 0.7908 (mtm) cc_final: 0.7668 (mtp) REVERT: B 65 THR cc_start: 0.7855 (m) cc_final: 0.7448 (p) REVERT: B 175 GLN cc_start: 0.7656 (pp30) cc_final: 0.7366 (pp30) REVERT: B 237 ASN cc_start: 0.8050 (p0) cc_final: 0.7815 (p0) REVERT: B 246 ASP cc_start: 0.8227 (t0) cc_final: 0.7566 (t0) REVERT: B 251 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.6499 (tpp80) REVERT: B 304 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7423 (ttp80) REVERT: B 339 TRP cc_start: 0.7553 (m100) cc_final: 0.7223 (m100) REVERT: C 15 LEU cc_start: 0.8077 (mt) cc_final: 0.7674 (mt) REVERT: R 52 LEU cc_start: 0.7240 (mt) cc_final: 0.6994 (mt) REVERT: R 54 MET cc_start: 0.6139 (ptp) cc_final: 0.5812 (ptp) REVERT: R 84 PHE cc_start: 0.6284 (m-80) cc_final: 0.5776 (m-80) REVERT: R 111 LEU cc_start: 0.7704 (tt) cc_final: 0.7472 (tp) REVERT: R 121 MET cc_start: 0.6982 (mtt) cc_final: 0.6677 (mtt) REVERT: R 173 PHE cc_start: 0.6633 (t80) cc_final: 0.6352 (t80) REVERT: R 183 ASN cc_start: 0.6207 (OUTLIER) cc_final: 0.5772 (p0) REVERT: R 184 GLN cc_start: 0.7449 (pm20) cc_final: 0.6193 (pm20) REVERT: R 187 ILE cc_start: 0.7163 (tp) cc_final: 0.6958 (tp) REVERT: R 201 ILE cc_start: 0.8049 (mt) cc_final: 0.7730 (mt) outliers start: 44 outliers final: 34 residues processed: 294 average time/residue: 0.2138 time to fit residues: 84.5913 Evaluate side-chains 312 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 277 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 410 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 313 ASN S 39 GLN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8763 Z= 0.212 Angle : 0.611 12.784 11917 Z= 0.312 Chirality : 0.043 0.214 1386 Planarity : 0.005 0.044 1484 Dihedral : 5.086 44.557 1226 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.59 % Allowed : 24.16 % Favored : 70.25 % 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: -0.67 (0.25), residues: 1104 helix: 0.78 (0.26), residues: 399 sheet: -0.92 (0.31), residues: 258 loop : -1.18 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.003 0.001 HIS S 155 PHE 0.020 0.002 PHE R 403 TYR 0.016 0.002 TYR B 264 ARG 0.002 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 289 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 35 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7454 (mtmm) REVERT: A 197 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7673 (mmmt) REVERT: A 198 MET cc_start: 0.6520 (ttm) cc_final: 0.6217 (ttm) REVERT: A 251 ASP cc_start: 0.7114 (t70) cc_final: 0.6544 (t0) REVERT: A 345 LYS cc_start: 0.8080 (tptt) cc_final: 0.7734 (tptt) REVERT: A 346 ASN cc_start: 0.8129 (m110) cc_final: 0.7697 (m110) REVERT: A 347 ASN cc_start: 0.7427 (m-40) cc_final: 0.6989 (m-40) REVERT: B 45 MET cc_start: 0.7866 (mtm) cc_final: 0.7649 (mtp) REVERT: B 65 THR cc_start: 0.7822 (m) cc_final: 0.7440 (p) REVERT: B 101 MET cc_start: 0.7451 (mtp) cc_final: 0.7176 (mtm) REVERT: B 132 ASN cc_start: 0.7648 (p0) cc_final: 0.7439 (p0) REVERT: B 170 ASP cc_start: 0.7123 (t0) cc_final: 0.6893 (t0) REVERT: B 175 GLN cc_start: 0.7669 (pp30) cc_final: 0.7378 (pp30) REVERT: B 234 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: B 237 ASN cc_start: 0.8039 (p0) cc_final: 0.7785 (p0) REVERT: B 246 ASP cc_start: 0.8220 (t0) cc_final: 0.7576 (t0) REVERT: B 253 PHE cc_start: 0.7781 (m-10) cc_final: 0.7371 (m-80) REVERT: B 304 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7357 (ttp80) REVERT: B 339 TRP cc_start: 0.7565 (m100) cc_final: 0.7172 (m100) REVERT: C 15 LEU cc_start: 0.8098 (mt) cc_final: 0.7693 (mt) REVERT: S 34 MET cc_start: 0.6317 (mmm) cc_final: 0.6059 (mmm) REVERT: S 190 ARG cc_start: 0.6566 (ptt-90) cc_final: 0.6364 (ptt-90) REVERT: R 52 LEU cc_start: 0.7223 (mt) cc_final: 0.6979 (mt) REVERT: R 54 MET cc_start: 0.6141 (ptp) cc_final: 0.5807 (ptp) REVERT: R 84 PHE cc_start: 0.6198 (m-80) cc_final: 0.5703 (m-80) REVERT: R 111 LEU cc_start: 0.7675 (tt) cc_final: 0.7436 (tp) REVERT: R 121 MET cc_start: 0.6967 (mtt) cc_final: 0.6659 (mtt) REVERT: R 140 TYR cc_start: 0.8101 (t80) cc_final: 0.7686 (t80) REVERT: R 173 PHE cc_start: 0.6618 (t80) cc_final: 0.6353 (t80) REVERT: R 184 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: R 187 ILE cc_start: 0.7187 (tp) cc_final: 0.6985 (tp) REVERT: R 201 ILE cc_start: 0.8070 (mt) cc_final: 0.7748 (mt) REVERT: R 218 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6922 (tt) outliers start: 50 outliers final: 38 residues processed: 301 average time/residue: 0.2182 time to fit residues: 88.3201 Evaluate side-chains 325 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 284 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 122 ASN Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 437 ILE Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 0.0070 chunk 105 optimal weight: 0.0870 chunk 65 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 88 ASN B 259 GLN S 82 GLN S 167 GLN ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8763 Z= 0.184 Angle : 0.602 10.654 11917 Z= 0.307 Chirality : 0.042 0.209 1386 Planarity : 0.004 0.043 1484 Dihedral : 4.960 45.698 1226 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.70 % Allowed : 26.40 % Favored : 68.90 % 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: -0.58 (0.25), residues: 1104 helix: 0.86 (0.26), residues: 399 sheet: -0.81 (0.31), residues: 257 loop : -1.18 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 311 PHE 0.023 0.001 PHE S 227 TYR 0.023 0.002 TYR R 131 ARG 0.003 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 284 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 35 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7454 (mtmm) REVERT: A 198 MET cc_start: 0.6555 (ttm) cc_final: 0.6249 (ttm) REVERT: A 251 ASP cc_start: 0.7063 (t70) cc_final: 0.6477 (t0) REVERT: A 304 GLN cc_start: 0.7325 (tp40) cc_final: 0.6996 (tp40) REVERT: A 345 LYS cc_start: 0.8138 (tptt) cc_final: 0.7803 (tptt) REVERT: A 347 ASN cc_start: 0.7431 (m-40) cc_final: 0.6957 (m-40) REVERT: B 45 MET cc_start: 0.7817 (mtm) cc_final: 0.7614 (mtp) REVERT: B 65 THR cc_start: 0.7771 (m) cc_final: 0.7423 (p) REVERT: B 132 ASN cc_start: 0.7611 (p0) cc_final: 0.7351 (p0) REVERT: B 170 ASP cc_start: 0.7108 (t0) cc_final: 0.6900 (t0) REVERT: B 175 GLN cc_start: 0.7632 (pp30) cc_final: 0.7334 (pp30) REVERT: B 207 SER cc_start: 0.6592 (t) cc_final: 0.6391 (p) REVERT: B 234 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: B 237 ASN cc_start: 0.7988 (p0) cc_final: 0.7756 (p0) REVERT: B 246 ASP cc_start: 0.8200 (t0) cc_final: 0.7554 (t0) REVERT: B 253 PHE cc_start: 0.7778 (m-10) cc_final: 0.7331 (m-80) REVERT: B 339 TRP cc_start: 0.7584 (m100) cc_final: 0.7058 (m100) REVERT: C 11 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 15 LEU cc_start: 0.8099 (mt) cc_final: 0.7444 (mt) REVERT: S 34 MET cc_start: 0.6379 (mmm) cc_final: 0.5989 (mmm) REVERT: S 165 PHE cc_start: 0.7410 (m-80) cc_final: 0.7179 (m-10) REVERT: R 52 LEU cc_start: 0.7193 (mt) cc_final: 0.6952 (mt) REVERT: R 54 MET cc_start: 0.6118 (ptp) cc_final: 0.5783 (ptp) REVERT: R 84 PHE cc_start: 0.6149 (m-80) cc_final: 0.5638 (m-80) REVERT: R 89 TYR cc_start: 0.6906 (t80) cc_final: 0.6546 (t80) REVERT: R 121 MET cc_start: 0.6936 (mtt) cc_final: 0.6626 (mtt) REVERT: R 140 TYR cc_start: 0.8100 (t80) cc_final: 0.7688 (t80) REVERT: R 173 PHE cc_start: 0.6573 (t80) cc_final: 0.6313 (t80) REVERT: R 183 ASN cc_start: 0.6118 (OUTLIER) cc_final: 0.5632 (p0) REVERT: R 184 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6318 (pm20) REVERT: R 187 ILE cc_start: 0.7193 (tp) cc_final: 0.6992 (tp) REVERT: R 201 ILE cc_start: 0.8110 (mt) cc_final: 0.7789 (mt) REVERT: R 214 LEU cc_start: 0.6944 (tp) cc_final: 0.6710 (tp) outliers start: 42 outliers final: 33 residues processed: 297 average time/residue: 0.2096 time to fit residues: 83.7972 Evaluate side-chains 311 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 275 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 437 ILE Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 0.0050 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 213 HIS B 259 GLN S 39 GLN S 167 GLN ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8763 Z= 0.233 Angle : 0.628 10.117 11917 Z= 0.322 Chirality : 0.043 0.220 1386 Planarity : 0.005 0.042 1484 Dihedral : 4.993 46.480 1226 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.37 % Allowed : 26.06 % Favored : 68.57 % 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: -0.68 (0.25), residues: 1104 helix: 0.86 (0.26), residues: 393 sheet: -0.92 (0.31), residues: 263 loop : -1.25 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS B 311 PHE 0.017 0.002 PHE S 227 TYR 0.017 0.002 TYR R 131 ARG 0.006 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 278 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 35 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7387 (mtmm) REVERT: A 198 MET cc_start: 0.6581 (ttm) cc_final: 0.6269 (ttm) REVERT: A 251 ASP cc_start: 0.7051 (t70) cc_final: 0.6471 (t0) REVERT: A 274 PHE cc_start: 0.6556 (t80) cc_final: 0.5998 (t80) REVERT: A 304 GLN cc_start: 0.7327 (tp40) cc_final: 0.7004 (tp40) REVERT: A 345 LYS cc_start: 0.8145 (tptt) cc_final: 0.7812 (tptt) REVERT: A 347 ASN cc_start: 0.7420 (m-40) cc_final: 0.7131 (m-40) REVERT: B 65 THR cc_start: 0.7804 (m) cc_final: 0.7420 (p) REVERT: B 101 MET cc_start: 0.7681 (mtt) cc_final: 0.7418 (mtp) REVERT: B 132 ASN cc_start: 0.7596 (p0) cc_final: 0.7325 (p0) REVERT: B 170 ASP cc_start: 0.7115 (t0) cc_final: 0.6914 (t0) REVERT: B 175 GLN cc_start: 0.7656 (pp30) cc_final: 0.7339 (pp30) REVERT: B 207 SER cc_start: 0.6635 (t) cc_final: 0.6426 (p) REVERT: B 234 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: B 237 ASN cc_start: 0.8119 (p0) cc_final: 0.7889 (p0) REVERT: B 246 ASP cc_start: 0.8225 (t0) cc_final: 0.7592 (t0) REVERT: B 251 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6074 (tpp80) REVERT: B 253 PHE cc_start: 0.7786 (m-10) cc_final: 0.7300 (m-80) REVERT: B 292 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: C 11 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7609 (tm-30) REVERT: C 15 LEU cc_start: 0.8116 (mt) cc_final: 0.7454 (mt) REVERT: S 34 MET cc_start: 0.6496 (mmm) cc_final: 0.5982 (mmm) REVERT: R 52 LEU cc_start: 0.7203 (mt) cc_final: 0.6960 (mt) REVERT: R 54 MET cc_start: 0.6137 (ptp) cc_final: 0.5845 (ptp) REVERT: R 84 PHE cc_start: 0.6176 (m-80) cc_final: 0.5687 (m-80) REVERT: R 89 TYR cc_start: 0.6952 (t80) cc_final: 0.6581 (t80) REVERT: R 121 MET cc_start: 0.6936 (mtt) cc_final: 0.6638 (mtt) REVERT: R 140 TYR cc_start: 0.8152 (t80) cc_final: 0.7758 (t80) REVERT: R 173 PHE cc_start: 0.6653 (t80) cc_final: 0.6376 (t80) REVERT: R 183 ASN cc_start: 0.6143 (OUTLIER) cc_final: 0.5652 (p0) REVERT: R 184 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6284 (pm20) REVERT: R 187 ILE cc_start: 0.7222 (tp) cc_final: 0.7017 (tp) REVERT: R 201 ILE cc_start: 0.8157 (mt) cc_final: 0.7834 (mt) outliers start: 48 outliers final: 36 residues processed: 293 average time/residue: 0.2149 time to fit residues: 85.0069 Evaluate side-chains 313 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 273 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 437 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 76 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.0050 chunk 64 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 213 HIS B 142 HIS B 259 GLN B 313 ASN S 167 GLN ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8763 Z= 0.195 Angle : 0.645 11.099 11917 Z= 0.325 Chirality : 0.043 0.223 1386 Planarity : 0.004 0.042 1484 Dihedral : 4.997 46.745 1226 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.92 % Allowed : 26.62 % Favored : 68.46 % 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: -0.64 (0.25), residues: 1104 helix: 0.87 (0.26), residues: 393 sheet: -0.83 (0.31), residues: 262 loop : -1.25 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 PHE 0.027 0.002 PHE R 128 TYR 0.017 0.001 TYR S 163 ARG 0.002 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7442 (tm-30) REVERT: A 35 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7367 (mtmm) REVERT: A 197 LYS cc_start: 0.8196 (mmtp) cc_final: 0.7939 (mmtm) REVERT: A 198 MET cc_start: 0.6548 (ttm) cc_final: 0.6274 (ttm) REVERT: A 251 ASP cc_start: 0.6984 (t70) cc_final: 0.6417 (t0) REVERT: A 304 GLN cc_start: 0.7273 (tp40) cc_final: 0.6942 (tp40) REVERT: A 345 LYS cc_start: 0.8137 (tptt) cc_final: 0.7794 (tptt) REVERT: A 347 ASN cc_start: 0.7411 (m-40) cc_final: 0.6935 (m-40) REVERT: A 353 LEU cc_start: 0.8297 (tp) cc_final: 0.8086 (tt) REVERT: B 65 THR cc_start: 0.7753 (m) cc_final: 0.7404 (p) REVERT: B 132 ASN cc_start: 0.7583 (p0) cc_final: 0.7289 (p0) REVERT: B 175 GLN cc_start: 0.7637 (pp30) cc_final: 0.7303 (pp30) REVERT: B 234 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: B 237 ASN cc_start: 0.8003 (p0) cc_final: 0.7748 (p0) REVERT: B 246 ASP cc_start: 0.8218 (t0) cc_final: 0.7569 (t0) REVERT: B 251 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6030 (tpp80) REVERT: B 292 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: C 11 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 15 LEU cc_start: 0.8103 (mt) cc_final: 0.7443 (mt) REVERT: S 34 MET cc_start: 0.6513 (mmm) cc_final: 0.5938 (mmm) REVERT: R 52 LEU cc_start: 0.7190 (mt) cc_final: 0.6924 (mt) REVERT: R 54 MET cc_start: 0.6110 (ptp) cc_final: 0.5822 (ptp) REVERT: R 84 PHE cc_start: 0.6151 (m-80) cc_final: 0.5662 (m-80) REVERT: R 89 TYR cc_start: 0.6956 (t80) cc_final: 0.6595 (t80) REVERT: R 121 MET cc_start: 0.6895 (mtt) cc_final: 0.6628 (mtt) REVERT: R 140 TYR cc_start: 0.8118 (t80) cc_final: 0.7760 (t80) REVERT: R 173 PHE cc_start: 0.6595 (t80) cc_final: 0.6324 (t80) REVERT: R 183 ASN cc_start: 0.6098 (OUTLIER) cc_final: 0.5609 (p0) REVERT: R 184 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: R 187 ILE cc_start: 0.7224 (tp) cc_final: 0.7022 (tp) REVERT: R 201 ILE cc_start: 0.8114 (mt) cc_final: 0.7803 (mt) outliers start: 44 outliers final: 35 residues processed: 292 average time/residue: 0.2202 time to fit residues: 85.8515 Evaluate side-chains 314 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 275 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 437 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 0.0770 chunk 99 optimal weight: 0.0170 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 259 GLN S 157 ASN ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8763 Z= 0.210 Angle : 0.663 11.212 11917 Z= 0.334 Chirality : 0.044 0.214 1386 Planarity : 0.005 0.045 1484 Dihedral : 5.013 47.166 1226 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.81 % Allowed : 27.18 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1104 helix: 0.88 (0.26), residues: 393 sheet: -0.97 (0.30), residues: 272 loop : -1.21 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.005 0.001 HIS B 311 PHE 0.029 0.002 PHE R 128 TYR 0.018 0.002 TYR S 163 ARG 0.003 0.000 ARG R 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 279 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 35 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7359 (mtmm) REVERT: A 197 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7950 (mmtm) REVERT: A 198 MET cc_start: 0.6549 (ttm) cc_final: 0.6286 (ttm) REVERT: A 251 ASP cc_start: 0.6954 (t70) cc_final: 0.6392 (t0) REVERT: A 274 PHE cc_start: 0.6460 (t80) cc_final: 0.6023 (t80) REVERT: A 304 GLN cc_start: 0.7264 (tp40) cc_final: 0.6938 (tp40) REVERT: A 345 LYS cc_start: 0.8131 (tptt) cc_final: 0.7791 (tptt) REVERT: A 347 ASN cc_start: 0.7401 (m-40) cc_final: 0.6929 (m-40) REVERT: A 353 LEU cc_start: 0.8206 (tp) cc_final: 0.7996 (tt) REVERT: B 65 THR cc_start: 0.7750 (m) cc_final: 0.7407 (p) REVERT: B 132 ASN cc_start: 0.7573 (p0) cc_final: 0.7282 (p0) REVERT: B 156 GLN cc_start: 0.6868 (mt0) cc_final: 0.6642 (mt0) REVERT: B 175 GLN cc_start: 0.7659 (pp30) cc_final: 0.7311 (pp30) REVERT: B 234 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: B 237 ASN cc_start: 0.8010 (p0) cc_final: 0.7788 (p0) REVERT: B 246 ASP cc_start: 0.8216 (t0) cc_final: 0.7562 (t0) REVERT: B 292 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: C 11 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 15 LEU cc_start: 0.8095 (mt) cc_final: 0.7440 (mt) REVERT: S 34 MET cc_start: 0.6554 (mmm) cc_final: 0.5976 (mmm) REVERT: R 52 LEU cc_start: 0.7188 (mt) cc_final: 0.6923 (mt) REVERT: R 54 MET cc_start: 0.6111 (ptp) cc_final: 0.5820 (ptp) REVERT: R 84 PHE cc_start: 0.6137 (m-80) cc_final: 0.5647 (m-80) REVERT: R 89 TYR cc_start: 0.6957 (t80) cc_final: 0.6591 (t80) REVERT: R 121 MET cc_start: 0.6904 (mtt) cc_final: 0.6612 (mtt) REVERT: R 173 PHE cc_start: 0.6608 (t80) cc_final: 0.6332 (t80) REVERT: R 183 ASN cc_start: 0.6151 (OUTLIER) cc_final: 0.5656 (p0) REVERT: R 184 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: R 187 ILE cc_start: 0.7138 (tp) cc_final: 0.6933 (tp) REVERT: R 201 ILE cc_start: 0.8116 (mt) cc_final: 0.7801 (mt) REVERT: R 218 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7145 (tt) outliers start: 43 outliers final: 35 residues processed: 294 average time/residue: 0.2194 time to fit residues: 86.5680 Evaluate side-chains 315 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.0570 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 259 GLN S 39 GLN S 157 ASN S 167 GLN ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.154797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135820 restraints weight = 14194.246| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.94 r_work: 0.3699 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8763 Z= 0.231 Angle : 0.663 11.302 11917 Z= 0.334 Chirality : 0.044 0.210 1386 Planarity : 0.005 0.042 1484 Dihedral : 5.045 47.479 1226 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.92 % Allowed : 27.29 % Favored : 67.79 % 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: -0.67 (0.25), residues: 1104 helix: 0.88 (0.26), residues: 393 sheet: -0.95 (0.30), residues: 272 loop : -1.24 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.007 0.001 HIS B 311 PHE 0.027 0.002 PHE R 128 TYR 0.020 0.002 TYR S 163 ARG 0.002 0.000 ARG B 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.55 seconds wall clock time: 47 minutes 2.84 seconds (2822.84 seconds total)