Starting phenix.real_space_refine on Thu Jan 18 13:33:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/01_2024/6k42_9912_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/01_2024/6k42_9912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/01_2024/6k42_9912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/01_2024/6k42_9912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/01_2024/6k42_9912_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/01_2024/6k42_9912_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5630 2.51 5 N 1510 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 116": "NH1" <-> "NH2" Residue "R ARG 128": "NH1" <-> "NH2" Residue "R ARG 359": "NH1" <-> "NH2" Residue "R PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8816 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1759 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2201 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 3 Chain: "H" Number of atoms: 1801 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 1828 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.87, per 1000 atoms: 0.67 Number of scatterers: 8816 At special positions: 0 Unit cell: (112.08, 110.679, 128.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1618 8.00 N 1510 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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: 3.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 14 sheets defined 29.8% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 4.114A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.871A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.823A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.527A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.770A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 4.101A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 13 through 38 removed outlier: 3.878A pdb=" N ASN R 30 " --> pdb=" O THR R 26 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 73 removed outlier: 3.729A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 84 through 115 removed outlier: 3.733A pdb=" N CYS R 96 " --> pdb=" O ASP R 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER R 99 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL R 114 " --> pdb=" O ARG R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 121 No H-bonds generated for 'chain 'R' and resid 118 through 121' Processing helix chain 'R' and resid 126 through 145 Processing helix chain 'R' and resid 170 through 180 removed outlier: 3.858A pdb=" N LEU R 174 " --> pdb=" O ALA R 170 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 203 removed outlier: 3.704A pdb=" N ASN R 203 " --> pdb=" O ALA R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 396 removed outlier: 3.632A pdb=" N THR R 364 " --> pdb=" O ARG R 360 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG R 365 " --> pdb=" O ALA R 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 377 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE R 380 " --> pdb=" O VAL R 376 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Proline residue: R 386 - end of helix removed outlier: 3.877A pdb=" N GLY R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA R 395 " --> pdb=" O TYR R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 428 removed outlier: 3.984A pdb=" N ASN R 418 " --> pdb=" O ILE R 414 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix removed outlier: 3.745A pdb=" N TYR R 426 " --> pdb=" O ASN R 422 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR R 427 " --> pdb=" O PRO R 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE R 428 " --> pdb=" O VAL R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 441 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.261A pdb=" N ALA A 220 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU A 39 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE A 222 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR A 320 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 268 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS A 322 " --> pdb=" O LEU A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 186 through 190 Processing sheet with id= C, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.840A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.527A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.168A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.114A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 190 through 192 Processing sheet with id= H, first strand: chain 'B' and resid 262 through 265 removed outlier: 3.680A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 294 through 297 Processing sheet with id= J, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= K, first strand: chain 'H' and resid 93 through 99 removed outlier: 3.754A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 128 through 130 removed outlier: 3.642A pdb=" N ARG H 148 " --> pdb=" O THR H 129 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 213 through 219 removed outlier: 5.557A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 191 through 196 296 hydrogen bonds defined for protein. 864 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: 2.22 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2622 1.34 - 1.46: 1721 1.46 - 1.58: 4582 1.58 - 1.70: 1 1.70 - 1.82: 79 Bond restraints: 9005 Sorted by residual: bond pdb=" C09 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C11 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.386 1.528 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C08 CZX R 501 " pdb=" C11 CZX R 501 " ideal model delta sigma weight residual 1.392 1.528 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C04 CZX R 501 " pdb=" C09 CZX R 501 " ideal model delta sigma weight residual 1.393 1.526 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C04 CZX R 501 " pdb=" C05 CZX R 501 " ideal model delta sigma weight residual 1.403 1.530 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 9000 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.33: 194 106.33 - 113.26: 4781 113.26 - 120.18: 3325 120.18 - 127.11: 3792 127.11 - 134.03: 99 Bond angle restraints: 12191 Sorted by residual: angle pdb=" N ILE R 396 " pdb=" CA ILE R 396 " pdb=" C ILE R 396 " ideal model delta sigma weight residual 110.82 101.31 9.51 9.70e-01 1.06e+00 9.61e+01 angle pdb=" C ASN H 157 " pdb=" N GLY H 158 " pdb=" CA GLY H 158 " ideal model delta sigma weight residual 121.70 131.39 -9.69 1.80e+00 3.09e-01 2.90e+01 angle pdb=" C TYR R 79 " pdb=" N PHE R 80 " pdb=" CA PHE R 80 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C PHE R 80 " pdb=" N ARG R 81 " pdb=" CA ARG R 81 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" CA ALA R 395 " pdb=" C ALA R 395 " pdb=" N ILE R 396 " ideal model delta sigma weight residual 118.81 113.25 5.56 1.15e+00 7.56e-01 2.34e+01 ... (remaining 12186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 5108 14.97 - 29.95: 173 29.95 - 44.92: 56 44.92 - 59.89: 8 59.89 - 74.86: 3 Dihedral angle restraints: 5348 sinusoidal: 2102 harmonic: 3246 Sorted by residual: dihedral pdb=" CA PRO R 146 " pdb=" C PRO R 146 " pdb=" N PRO R 147 " pdb=" CA PRO R 147 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ILE A 19 " pdb=" C ILE A 19 " pdb=" N ASP A 20 " pdb=" CA ASP A 20 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.10 33.90 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 5345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1139 0.061 - 0.123: 198 0.123 - 0.184: 32 0.184 - 0.246: 2 0.246 - 0.307: 2 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ILE R 396 " pdb=" N ILE R 396 " pdb=" C ILE R 396 " pdb=" CB ILE R 396 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C03 CZX R 501 " pdb=" C04 CZX R 501 " pdb=" C06 CZX R 501 " pdb=" C07 CZX R 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA CYS R 397 " pdb=" N CYS R 397 " pdb=" C CYS R 397 " pdb=" CB CYS R 397 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1370 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 146 " 0.063 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO R 147 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO R 147 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 147 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C THR A 340 " 0.042 2.00e-02 2.50e+03 pdb=" O THR A 340 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 341 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 395 " 0.011 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C ALA R 395 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA R 395 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE R 396 " 0.014 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2389 2.81 - 3.33: 7268 3.33 - 3.86: 13820 3.86 - 4.38: 15445 4.38 - 4.90: 27047 Nonbonded interactions: 65969 Sorted by model distance: nonbonded pdb=" OG SER R 69 " pdb=" OH TYR R 88 " model vdw 2.288 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.302 2.440 nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.323 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.343 2.440 nonbonded pdb=" O CYS R 397 " pdb=" N CYS R 401 " model vdw 2.345 2.520 ... (remaining 65964 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.230 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 27.450 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 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 : 0.005 0.144 9005 Z= 0.319 Angle : 0.823 9.687 12191 Z= 0.478 Chirality : 0.049 0.307 1373 Planarity : 0.007 0.094 1537 Dihedral : 9.237 74.864 3241 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.31 % Allowed : 1.78 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.19), residues: 1095 helix: -2.64 (0.19), residues: 340 sheet: -2.22 (0.30), residues: 242 loop : -3.42 (0.21), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.010 0.001 HIS R 102 PHE 0.031 0.002 PHE R 369 TYR 0.017 0.002 TYR R 79 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7535 (pp) cc_final: 0.7222 (pp) REVERT: A 49 ILE cc_start: 0.6716 (pt) cc_final: 0.6462 (pt) REVERT: A 50 VAL cc_start: 0.6760 (m) cc_final: 0.6501 (m) REVERT: B 43 ILE cc_start: 0.7437 (mm) cc_final: 0.6307 (mm) REVERT: B 280 LYS cc_start: 0.6658 (tptt) cc_final: 0.6209 (tptm) REVERT: B 313 ASN cc_start: 0.7856 (t0) cc_final: 0.7340 (m-40) REVERT: R 102 HIS cc_start: 0.6568 (m-70) cc_final: 0.5985 (m-70) REVERT: R 414 ILE cc_start: 0.7376 (mm) cc_final: 0.7152 (mm) REVERT: R 429 PHE cc_start: 0.6872 (m-10) cc_final: 0.6657 (m-10) REVERT: H 58 ILE cc_start: 0.8045 (mt) cc_final: 0.7839 (mt) outliers start: 1 outliers final: 1 residues processed: 431 average time/residue: 0.2330 time to fit residues: 130.8001 Evaluate side-chains 283 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.0570 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 346 ASN B 16 ASN B 75 GLN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 295 ASN B 311 HIS R 30 ASN R 121 ASN R 362 GLN R 418 ASN H 155 HIS H 159 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9005 Z= 0.188 Angle : 0.593 7.015 12191 Z= 0.316 Chirality : 0.042 0.257 1373 Planarity : 0.005 0.079 1537 Dihedral : 4.562 17.917 1225 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.21 % Allowed : 2.41 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.22), residues: 1095 helix: -0.54 (0.26), residues: 335 sheet: -1.83 (0.31), residues: 244 loop : -2.94 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 84 HIS 0.009 0.001 HIS H 155 PHE 0.033 0.002 PHE R 369 TYR 0.016 0.002 TYR H 178 ARG 0.010 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7862 (pt) cc_final: 0.7479 (mt) REVERT: A 198 MET cc_start: 0.7427 (tpp) cc_final: 0.6966 (ttm) REVERT: A 246 SER cc_start: 0.8688 (m) cc_final: 0.8305 (m) REVERT: B 68 ARG cc_start: 0.7840 (tpt-90) cc_final: 0.7179 (ttt-90) REVERT: B 280 LYS cc_start: 0.7142 (tptt) cc_final: 0.6573 (tptm) REVERT: B 313 ASN cc_start: 0.7784 (t0) cc_final: 0.7540 (m-40) REVERT: B 322 ASP cc_start: 0.6025 (t0) cc_final: 0.5761 (t0) REVERT: R 65 ILE cc_start: 0.7932 (mm) cc_final: 0.7692 (tt) REVERT: R 414 ILE cc_start: 0.7483 (mm) cc_final: 0.7140 (mm) REVERT: R 418 ASN cc_start: 0.5265 (t0) cc_final: 0.4726 (t0) REVERT: H 39 GLN cc_start: 0.6668 (tp40) cc_final: 0.5982 (tt0) REVERT: H 96 CYS cc_start: 0.4005 (p) cc_final: 0.3801 (p) REVERT: H 176 LEU cc_start: 0.8502 (mt) cc_final: 0.8293 (mt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1891 time to fit residues: 84.7572 Evaluate side-chains 265 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 346 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 266 HIS R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 GLN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9005 Z= 0.222 Angle : 0.650 9.295 12191 Z= 0.342 Chirality : 0.044 0.160 1373 Planarity : 0.005 0.072 1537 Dihedral : 4.705 18.829 1225 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.42 % Allowed : 2.30 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.24), residues: 1095 helix: 0.16 (0.27), residues: 334 sheet: -1.59 (0.33), residues: 235 loop : -2.54 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 111 HIS 0.008 0.002 HIS H 155 PHE 0.026 0.002 PHE R 369 TYR 0.015 0.002 TYR H 216 ARG 0.004 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 331 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8360 (pt) cc_final: 0.8135 (mt) REVERT: A 210 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7975 (mmmt) REVERT: A 227 LEU cc_start: 0.7291 (mt) cc_final: 0.6915 (mt) REVERT: A 246 SER cc_start: 0.8881 (m) cc_final: 0.8509 (m) REVERT: A 346 ASN cc_start: 0.8478 (m110) cc_final: 0.8189 (m110) REVERT: B 75 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7439 (mm-40) REVERT: B 251 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7869 (mtt-85) REVERT: B 258 ASP cc_start: 0.7348 (t0) cc_final: 0.7064 (t0) REVERT: B 261 LEU cc_start: 0.8249 (mt) cc_final: 0.8006 (mt) REVERT: B 280 LYS cc_start: 0.6883 (tptt) cc_final: 0.6404 (tmtt) REVERT: B 313 ASN cc_start: 0.8105 (t0) cc_final: 0.7834 (m-40) REVERT: R 25 PHE cc_start: 0.5894 (m-80) cc_final: 0.5691 (m-80) REVERT: R 362 GLN cc_start: 0.6295 (pp30) cc_final: 0.5858 (pp30) REVERT: R 370 THR cc_start: 0.7226 (p) cc_final: 0.6983 (t) REVERT: R 414 ILE cc_start: 0.8082 (mm) cc_final: 0.7791 (mm) REVERT: H 29 PHE cc_start: 0.8893 (t80) cc_final: 0.8615 (t80) REVERT: H 58 ILE cc_start: 0.8236 (mt) cc_final: 0.8031 (mt) REVERT: H 82 GLN cc_start: 0.6688 (pm20) cc_final: 0.5774 (mp10) REVERT: H 103 TYR cc_start: 0.7599 (t80) cc_final: 0.7385 (t80) REVERT: H 180 MET cc_start: 0.7012 (ttt) cc_final: 0.6667 (ttp) REVERT: H 218 MET cc_start: 0.8603 (tmm) cc_final: 0.8343 (ttt) outliers start: 2 outliers final: 0 residues processed: 332 average time/residue: 0.2191 time to fit residues: 97.9755 Evaluate side-chains 262 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN G 11 GLN R 30 ASN R 102 HIS ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9005 Z= 0.239 Angle : 0.636 7.316 12191 Z= 0.333 Chirality : 0.044 0.263 1373 Planarity : 0.004 0.068 1537 Dihedral : 4.679 17.630 1225 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.31 % Allowed : 2.30 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.24), residues: 1095 helix: 0.37 (0.28), residues: 335 sheet: -1.35 (0.33), residues: 240 loop : -2.45 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.015 0.002 HIS R 102 PHE 0.028 0.002 PHE R 369 TYR 0.019 0.002 TYR B 59 ARG 0.006 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8597 (pt) cc_final: 0.8297 (mt) REVERT: A 210 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8165 (mmmt) REVERT: A 337 ASP cc_start: 0.7269 (t0) cc_final: 0.7061 (t0) REVERT: A 346 ASN cc_start: 0.8214 (m110) cc_final: 0.7831 (m-40) REVERT: B 86 THR cc_start: 0.7993 (p) cc_final: 0.7537 (p) REVERT: B 88 ASN cc_start: 0.8653 (m-40) cc_final: 0.8123 (m-40) REVERT: B 251 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7956 (mtt-85) REVERT: B 280 LYS cc_start: 0.7317 (tptt) cc_final: 0.6668 (tmtt) REVERT: B 313 ASN cc_start: 0.8215 (t0) cc_final: 0.7991 (m-40) REVERT: B 322 ASP cc_start: 0.6502 (t0) cc_final: 0.6226 (t0) REVERT: R 102 HIS cc_start: 0.7509 (m90) cc_final: 0.7097 (m90) REVERT: R 107 SER cc_start: 0.8463 (t) cc_final: 0.8226 (t) REVERT: R 362 GLN cc_start: 0.6280 (pp30) cc_final: 0.5889 (pp30) REVERT: R 377 ILE cc_start: 0.8131 (tp) cc_final: 0.7928 (tp) REVERT: R 414 ILE cc_start: 0.8070 (mm) cc_final: 0.7840 (mm) REVERT: R 427 THR cc_start: 0.8594 (p) cc_final: 0.8349 (p) REVERT: H 82 GLN cc_start: 0.6450 (pm20) cc_final: 0.5584 (mp10) REVERT: H 93 MET cc_start: 0.6332 (tpp) cc_final: 0.4719 (ttt) REVERT: H 95 TYR cc_start: 0.7640 (m-80) cc_final: 0.7325 (m-80) REVERT: H 115 THR cc_start: 0.7754 (p) cc_final: 0.7409 (p) REVERT: H 127 VAL cc_start: 0.7382 (t) cc_final: 0.7158 (t) REVERT: H 176 LEU cc_start: 0.8535 (mt) cc_final: 0.8333 (mt) REVERT: H 180 MET cc_start: 0.7000 (ttt) cc_final: 0.6717 (ttp) REVERT: H 206 ARG cc_start: 0.7584 (ptt90) cc_final: 0.7261 (mmp-170) REVERT: H 218 MET cc_start: 0.8697 (tmm) cc_final: 0.8111 (ttt) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.2215 time to fit residues: 98.9021 Evaluate side-chains 265 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 237 ASN B 239 ASN G 11 GLN R 30 ASN R 121 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9005 Z= 0.211 Angle : 0.620 7.550 12191 Z= 0.324 Chirality : 0.044 0.259 1373 Planarity : 0.004 0.070 1537 Dihedral : 4.619 18.565 1225 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.21 % Allowed : 1.68 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1095 helix: 0.44 (0.28), residues: 338 sheet: -1.35 (0.32), residues: 249 loop : -2.34 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 111 HIS 0.004 0.001 HIS B 183 PHE 0.028 0.002 PHE R 369 TYR 0.015 0.002 TYR B 59 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 1.008 Fit side-chains REVERT: A 19 ILE cc_start: 0.8735 (pt) cc_final: 0.8447 (mt) REVERT: A 210 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8106 (mmmt) REVERT: B 44 GLN cc_start: 0.6943 (mm-40) cc_final: 0.6727 (mp10) REVERT: B 67 SER cc_start: 0.8822 (m) cc_final: 0.8118 (t) REVERT: B 86 THR cc_start: 0.8303 (p) cc_final: 0.7680 (p) REVERT: B 88 ASN cc_start: 0.8654 (m-40) cc_final: 0.8086 (m-40) REVERT: B 169 TRP cc_start: 0.8250 (m100) cc_final: 0.7979 (m100) REVERT: B 209 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7891 (mmtp) REVERT: B 280 LYS cc_start: 0.7325 (tptt) cc_final: 0.6746 (tmtt) REVERT: B 313 ASN cc_start: 0.8294 (t0) cc_final: 0.8011 (m-40) REVERT: B 322 ASP cc_start: 0.6596 (t0) cc_final: 0.6066 (t0) REVERT: R 44 ARG cc_start: 0.8412 (mtt180) cc_final: 0.8211 (mtt180) REVERT: R 98 SER cc_start: 0.8662 (p) cc_final: 0.7819 (p) REVERT: R 102 HIS cc_start: 0.7542 (m90) cc_final: 0.6915 (m90) REVERT: R 362 GLN cc_start: 0.6421 (pp30) cc_final: 0.5912 (pp30) REVERT: R 377 ILE cc_start: 0.8276 (tp) cc_final: 0.7870 (tp) REVERT: R 414 ILE cc_start: 0.8057 (mm) cc_final: 0.7741 (mm) REVERT: R 427 THR cc_start: 0.8546 (p) cc_final: 0.8328 (p) REVERT: H 82 GLN cc_start: 0.6518 (pm20) cc_final: 0.5679 (mp10) REVERT: H 93 MET cc_start: 0.6345 (tpp) cc_final: 0.4758 (ttt) REVERT: H 115 THR cc_start: 0.7960 (p) cc_final: 0.7656 (p) REVERT: H 206 ARG cc_start: 0.7591 (ptt90) cc_final: 0.7122 (mmp80) REVERT: H 218 MET cc_start: 0.8725 (tmm) cc_final: 0.8167 (ttt) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2254 time to fit residues: 95.9226 Evaluate side-chains 268 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 183 HIS B 239 ASN B 295 ASN G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9005 Z= 0.258 Angle : 0.664 7.547 12191 Z= 0.348 Chirality : 0.045 0.259 1373 Planarity : 0.004 0.069 1537 Dihedral : 4.790 19.629 1225 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.21 % Allowed : 2.41 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.24), residues: 1095 helix: 0.33 (0.28), residues: 343 sheet: -1.37 (0.33), residues: 244 loop : -2.35 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP H 111 HIS 0.004 0.001 HIS G 44 PHE 0.028 0.002 PHE R 369 TYR 0.020 0.002 TYR R 416 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8916 (pt) cc_final: 0.8503 (mt) REVERT: A 210 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8177 (mmmt) REVERT: B 44 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6833 (mp10) REVERT: B 86 THR cc_start: 0.8408 (p) cc_final: 0.7779 (p) REVERT: B 88 ASN cc_start: 0.8734 (m-40) cc_final: 0.8180 (m-40) REVERT: B 169 TRP cc_start: 0.8354 (m100) cc_final: 0.7999 (m100) REVERT: B 209 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7561 (mmtp) REVERT: B 280 LYS cc_start: 0.7142 (tptt) cc_final: 0.6565 (tmtt) REVERT: B 313 ASN cc_start: 0.8369 (t0) cc_final: 0.8072 (m-40) REVERT: B 322 ASP cc_start: 0.6691 (t0) cc_final: 0.6458 (t0) REVERT: R 44 ARG cc_start: 0.8468 (mtt180) cc_final: 0.8257 (mtt180) REVERT: R 102 HIS cc_start: 0.7577 (m90) cc_final: 0.7097 (m90) REVERT: R 362 GLN cc_start: 0.6524 (pp30) cc_final: 0.6002 (pp30) REVERT: R 377 ILE cc_start: 0.8436 (tp) cc_final: 0.8102 (tp) REVERT: R 414 ILE cc_start: 0.8089 (mm) cc_final: 0.7714 (mm) REVERT: R 428 ILE cc_start: 0.7739 (tt) cc_final: 0.7529 (tp) REVERT: H 93 MET cc_start: 0.6570 (tpp) cc_final: 0.5583 (ttt) REVERT: H 115 THR cc_start: 0.8376 (p) cc_final: 0.8071 (p) REVERT: H 176 LEU cc_start: 0.8515 (mt) cc_final: 0.8300 (mt) REVERT: H 225 LEU cc_start: 0.8437 (mm) cc_final: 0.7910 (mm) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2188 time to fit residues: 92.2210 Evaluate side-chains 265 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.7255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9005 Z= 0.200 Angle : 0.634 7.585 12191 Z= 0.327 Chirality : 0.044 0.272 1373 Planarity : 0.004 0.058 1537 Dihedral : 4.623 17.986 1225 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.21 % Allowed : 1.57 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.25), residues: 1095 helix: 0.46 (0.28), residues: 344 sheet: -1.28 (0.32), residues: 259 loop : -2.34 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 111 HIS 0.004 0.001 HIS H 155 PHE 0.028 0.002 PHE R 369 TYR 0.016 0.002 TYR B 59 ARG 0.007 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8634 (pt) cc_final: 0.8384 (mt) REVERT: A 210 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8226 (mmmt) REVERT: A 330 LYS cc_start: 0.7398 (tptm) cc_final: 0.7142 (tptm) REVERT: B 44 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6892 (mp10) REVERT: B 57 LYS cc_start: 0.8241 (mttt) cc_final: 0.7986 (mttt) REVERT: B 86 THR cc_start: 0.8686 (p) cc_final: 0.8087 (p) REVERT: B 88 ASN cc_start: 0.8769 (m-40) cc_final: 0.8227 (m-40) REVERT: B 280 LYS cc_start: 0.6993 (tptt) cc_final: 0.6517 (tmtt) REVERT: B 313 ASN cc_start: 0.8389 (t0) cc_final: 0.7894 (m-40) REVERT: B 322 ASP cc_start: 0.6346 (t0) cc_final: 0.6103 (t0) REVERT: G 38 MET cc_start: 0.4995 (ptm) cc_final: 0.4383 (ptm) REVERT: R 44 ARG cc_start: 0.8403 (mtt180) cc_final: 0.8192 (mtt180) REVERT: R 102 HIS cc_start: 0.7645 (m90) cc_final: 0.7162 (m90) REVERT: R 362 GLN cc_start: 0.6456 (pp30) cc_final: 0.6007 (pp30) REVERT: R 377 ILE cc_start: 0.8511 (tp) cc_final: 0.8005 (tp) REVERT: R 382 LEU cc_start: 0.8475 (pp) cc_final: 0.8086 (tt) REVERT: R 414 ILE cc_start: 0.8073 (mm) cc_final: 0.7753 (mm) REVERT: R 428 ILE cc_start: 0.7752 (tt) cc_final: 0.7375 (tp) REVERT: H 93 MET cc_start: 0.6551 (tpp) cc_final: 0.5390 (ttt) REVERT: H 95 TYR cc_start: 0.7363 (m-10) cc_final: 0.7097 (m-10) REVERT: H 115 THR cc_start: 0.8179 (p) cc_final: 0.7943 (p) REVERT: H 189 ASP cc_start: 0.7274 (t0) cc_final: 0.7035 (t0) REVERT: H 225 LEU cc_start: 0.8345 (mm) cc_final: 0.7892 (mm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2346 time to fit residues: 103.5908 Evaluate side-chains 284 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 304 GLN A 333 GLN G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 155 HIS H 159 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.7581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9005 Z= 0.243 Angle : 0.668 9.226 12191 Z= 0.344 Chirality : 0.044 0.259 1373 Planarity : 0.004 0.054 1537 Dihedral : 4.757 19.934 1225 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.31 % Allowed : 1.15 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1095 helix: 0.39 (0.28), residues: 349 sheet: -1.14 (0.33), residues: 250 loop : -2.31 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 111 HIS 0.005 0.001 HIS H 155 PHE 0.028 0.002 PHE R 21 TYR 0.022 0.002 TYR H 215 ARG 0.007 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.9026 (pt) cc_final: 0.8523 (mt) REVERT: A 210 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8366 (mmmt) REVERT: B 30 LEU cc_start: 0.5561 (tt) cc_final: 0.4797 (tt) REVERT: B 44 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6933 (mp10) REVERT: B 86 THR cc_start: 0.8836 (p) cc_final: 0.8199 (p) REVERT: B 88 ASN cc_start: 0.8686 (m-40) cc_final: 0.8187 (m-40) REVERT: B 169 TRP cc_start: 0.8388 (m100) cc_final: 0.7954 (m100) REVERT: B 209 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7805 (mmtp) REVERT: B 260 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7856 (mt-10) REVERT: B 280 LYS cc_start: 0.7214 (tptt) cc_final: 0.6548 (tmtt) REVERT: B 313 ASN cc_start: 0.8415 (t0) cc_final: 0.7933 (m-40) REVERT: B 322 ASP cc_start: 0.6377 (t0) cc_final: 0.6128 (t0) REVERT: G 38 MET cc_start: 0.5013 (ptm) cc_final: 0.4535 (ptm) REVERT: R 83 THR cc_start: 0.7282 (p) cc_final: 0.7025 (p) REVERT: R 102 HIS cc_start: 0.7637 (m90) cc_final: 0.7113 (m90) REVERT: R 362 GLN cc_start: 0.6495 (pp30) cc_final: 0.6048 (pp30) REVERT: R 377 ILE cc_start: 0.8643 (tp) cc_final: 0.8172 (tp) REVERT: R 382 LEU cc_start: 0.8505 (pp) cc_final: 0.8125 (tt) REVERT: R 414 ILE cc_start: 0.8171 (mm) cc_final: 0.7799 (mm) REVERT: R 428 ILE cc_start: 0.7775 (tt) cc_final: 0.7413 (tp) REVERT: H 93 MET cc_start: 0.6606 (tpp) cc_final: 0.5470 (ttt) REVERT: H 95 TYR cc_start: 0.7075 (m-10) cc_final: 0.6814 (m-10) REVERT: H 115 THR cc_start: 0.8508 (p) cc_final: 0.8300 (p) REVERT: H 138 THR cc_start: 0.6919 (t) cc_final: 0.6502 (m) REVERT: H 176 LEU cc_start: 0.8632 (mt) cc_final: 0.8412 (mt) REVERT: H 225 LEU cc_start: 0.8437 (mm) cc_final: 0.7920 (mm) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.2173 time to fit residues: 94.3389 Evaluate side-chains 270 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 0.3980 chunk 59 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 176 GLN B 237 ASN G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 155 HIS ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.7677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9005 Z= 0.179 Angle : 0.640 8.333 12191 Z= 0.330 Chirality : 0.043 0.262 1373 Planarity : 0.004 0.061 1537 Dihedral : 4.547 18.244 1225 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.21 % Allowed : 0.84 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.25), residues: 1095 helix: 0.57 (0.29), residues: 350 sheet: -1.16 (0.33), residues: 261 loop : -2.27 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 111 HIS 0.010 0.001 HIS H 155 PHE 0.028 0.002 PHE R 412 TYR 0.031 0.002 TYR R 416 ARG 0.007 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8849 (pt) cc_final: 0.8429 (mt) REVERT: A 210 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8246 (mmmt) REVERT: B 86 THR cc_start: 0.8838 (p) cc_final: 0.8244 (p) REVERT: B 88 ASN cc_start: 0.8855 (m-40) cc_final: 0.8279 (m-40) REVERT: B 169 TRP cc_start: 0.8365 (m100) cc_final: 0.7945 (m100) REVERT: B 209 LYS cc_start: 0.7929 (mmmm) cc_final: 0.7703 (mmtp) REVERT: B 280 LYS cc_start: 0.6959 (tptt) cc_final: 0.6508 (tmtt) REVERT: B 313 ASN cc_start: 0.8235 (t0) cc_final: 0.7890 (m-40) REVERT: B 322 ASP cc_start: 0.6302 (t0) cc_final: 0.6050 (t0) REVERT: G 38 MET cc_start: 0.4974 (ptm) cc_final: 0.4321 (ptm) REVERT: R 98 SER cc_start: 0.8602 (p) cc_final: 0.7719 (p) REVERT: R 102 HIS cc_start: 0.7525 (m90) cc_final: 0.6991 (m90) REVERT: R 362 GLN cc_start: 0.6209 (pp30) cc_final: 0.5710 (pp30) REVERT: R 377 ILE cc_start: 0.8521 (tp) cc_final: 0.8160 (tp) REVERT: R 414 ILE cc_start: 0.8053 (mm) cc_final: 0.7609 (mm) REVERT: R 428 ILE cc_start: 0.7589 (tt) cc_final: 0.7230 (tp) REVERT: H 82 GLN cc_start: 0.6701 (pm20) cc_final: 0.6352 (pm20) REVERT: H 93 MET cc_start: 0.6551 (tpp) cc_final: 0.5402 (ttt) REVERT: H 95 TYR cc_start: 0.6980 (m-10) cc_final: 0.6729 (m-10) REVERT: H 138 THR cc_start: 0.7431 (t) cc_final: 0.6809 (m) REVERT: H 189 ASP cc_start: 0.7400 (t0) cc_final: 0.7123 (t0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2223 time to fit residues: 94.3171 Evaluate side-chains 278 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.917 > 50: distance: 147 - 151: 4.628 distance: 151 - 152: 10.612 distance: 152 - 153: 3.275 distance: 152 - 155: 4.043 distance: 153 - 154: 10.481 distance: 153 - 163: 7.713 distance: 155 - 156: 7.406 distance: 156 - 157: 3.830 distance: 156 - 158: 9.298 distance: 157 - 159: 7.396 distance: 159 - 161: 11.477 distance: 160 - 161: 10.847 distance: 161 - 162: 16.847 distance: 163 - 164: 17.857 distance: 163 - 169: 19.475 distance: 164 - 165: 39.881 distance: 164 - 167: 11.716 distance: 165 - 166: 19.494 distance: 165 - 170: 45.060 distance: 167 - 168: 17.222 distance: 168 - 169: 19.352 distance: 170 - 171: 22.377 distance: 171 - 172: 27.127 distance: 171 - 174: 30.349 distance: 172 - 173: 8.227 distance: 172 - 178: 12.809 distance: 174 - 175: 39.569 distance: 175 - 176: 15.224 distance: 175 - 177: 47.169 distance: 178 - 179: 6.291 distance: 179 - 182: 10.012 distance: 180 - 181: 22.134 distance: 180 - 185: 4.332 distance: 182 - 183: 12.677 distance: 182 - 184: 9.294 distance: 185 - 186: 13.777 distance: 186 - 187: 37.094 distance: 186 - 189: 34.555 distance: 187 - 188: 22.439 distance: 187 - 196: 13.721 distance: 189 - 190: 28.533 distance: 190 - 191: 13.136 distance: 190 - 192: 13.686 distance: 191 - 193: 17.690 distance: 192 - 194: 15.408 distance: 193 - 195: 10.757 distance: 194 - 195: 14.342 distance: 196 - 197: 18.344 distance: 197 - 198: 9.565 distance: 198 - 199: 21.478 distance: 198 - 200: 22.780 distance: 200 - 201: 19.641 distance: 201 - 202: 30.737 distance: 201 - 204: 22.629 distance: 202 - 203: 17.631 distance: 202 - 205: 9.522 distance: 205 - 206: 18.103 distance: 206 - 207: 7.852 distance: 207 - 208: 21.300 distance: 207 - 209: 13.508 distance: 209 - 210: 16.824 distance: 210 - 211: 7.709 distance: 210 - 213: 6.647 distance: 211 - 212: 23.155 distance: 211 - 216: 11.985 distance: 213 - 214: 5.626 distance: 213 - 215: 8.140 distance: 216 - 217: 12.370 distance: 217 - 220: 18.246 distance: 218 - 219: 9.041 distance: 218 - 225: 7.119 distance: 220 - 221: 12.281 distance: 221 - 222: 6.047 distance: 222 - 223: 5.195 distance: 223 - 224: 19.135