Starting phenix.real_space_refine on Sat Apr 6 23:49:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3o_41007/04_2024/8t3o_41007_updated.pdb" } resolution = 3.06 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= 0.035 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 55 5.16 5 C 5810 2.51 5 N 1561 2.21 5 O 1680 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 43": "OE1" <-> "OE2" Residue "R ARG 99": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "N ARG 72": "NH1" <-> "NH2" Residue "N ARG 192": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9109 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2363 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 2 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1797 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Unusual residues: {'2Y5': 1, 'PLM': 1, 'YN9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.18, per 1000 atoms: 0.57 Number of scatterers: 9109 At special positions: 0 Unit cell: (86.112, 122.544, 127.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 2 15.00 F 1 9.00 O 1680 8.00 N 1561 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " 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: 3.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'R' and resid 36 through 70 removed outlier: 4.193A pdb=" N ALA R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 88 Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 108 through 141 removed outlier: 4.102A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 175 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 217 through 243 removed outlier: 3.524A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 290 removed outlier: 3.824A pdb=" N GLN R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASP R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 300 through 320 removed outlier: 3.725A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN R 317 " --> pdb=" O ASN R 313 " (cutoff:3.500A) Proline residue: R 318 - end of helix 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 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.699A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 169 removed outlier: 4.340A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 169' Processing helix chain 'A' and resid 184 through 202 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 177 through 181 removed outlier: 3.551A pdb=" N ARG R 178 " --> pdb=" O THR R 195 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR R 195 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL R 180 " --> pdb=" O ILE R 193 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE R 193 " --> pdb=" O VAL R 180 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.868A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.726A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 4.077A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.659A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 3.676A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'A' and resid 105 through 111 removed outlier: 6.623A pdb=" N SER A 138 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 108 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 140 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL A 110 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE A 142 " --> pdb=" O VAL A 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'N' and resid 115 through 117 removed outlier: 5.718A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'N' and resid 147 through 149 removed outlier: 6.556A pdb=" N LYS N 245 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE N 190 " --> pdb=" O TRP N 177 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU N 188 " --> pdb=" O LEU N 179 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1119 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: 2.56 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1455 1.31 - 1.44: 2570 1.44 - 1.56: 5186 1.56 - 1.69: 4 1.69 - 1.81: 79 Bond restraints: 9294 Sorted by residual: bond pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.528 1.380 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.532 1.471 0.061 1.68e-02 3.54e+03 1.31e+01 bond pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.18e+01 bond pdb=" N CYS R 194 " pdb=" CA CYS R 194 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.19e-02 7.06e+03 1.15e+01 bond pdb=" N ILE R 193 " pdb=" CA ILE R 193 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.08e-02 8.57e+03 1.07e+01 ... (remaining 9289 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.43: 217 106.43 - 113.42: 5115 113.42 - 120.42: 3627 120.42 - 127.41: 3541 127.41 - 134.40: 99 Bond angle restraints: 12599 Sorted by residual: angle pdb=" C21 2Y5 R 402 " pdb=" C22 2Y5 R 402 " pdb=" C23 2Y5 R 402 " ideal model delta sigma weight residual 85.82 120.28 -34.46 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C18 2Y5 R 402 " pdb=" C19 2Y5 R 402 " pdb=" C20 2Y5 R 402 " ideal model delta sigma weight residual 152.65 120.31 32.34 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C15 2Y5 R 402 " pdb=" C16 2Y5 R 402 " pdb=" C17 2Y5 R 402 " ideal model delta sigma weight residual 152.62 120.40 32.22 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C24 2Y5 R 402 " pdb=" C25 2Y5 R 402 " pdb=" C26 2Y5 R 402 " ideal model delta sigma weight residual 152.70 120.50 32.20 3.00e+00 1.11e-01 1.15e+02 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 106.96 6.51 1.01e+00 9.80e-01 4.15e+01 ... (remaining 12594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 5229 29.54 - 59.07: 260 59.07 - 88.61: 23 88.61 - 118.15: 2 118.15 - 147.68: 2 Dihedral angle restraints: 5516 sinusoidal: 2161 harmonic: 3355 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual -86.00 -148.52 62.52 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" C24 2Y5 R 402 " pdb=" C25 2Y5 R 402 " pdb=" C26 2Y5 R 402 " pdb=" C27 2Y5 R 402 " ideal model delta sinusoidal sigma weight residual -30.76 -178.44 147.68 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C1 2Y5 R 402 " pdb=" O1 2Y5 R 402 " pdb=" P1 2Y5 R 402 " pdb=" O13 2Y5 R 402 " ideal model delta sinusoidal sigma weight residual 64.28 -162.22 -133.50 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1164 0.058 - 0.116: 217 0.116 - 0.174: 48 0.174 - 0.232: 9 0.232 - 0.290: 6 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CA ILE A 200 " pdb=" N ILE A 200 " pdb=" C ILE A 200 " pdb=" CB ILE A 200 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE R 193 " pdb=" N ILE R 193 " pdb=" C ILE R 193 " pdb=" CB ILE R 193 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1441 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 312 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP B 312 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP B 312 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 312 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO R 172 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 192 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ARG N 192 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG N 192 " 0.012 2.00e-02 2.50e+03 pdb=" N MET N 193 " 0.012 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 213 2.68 - 3.23: 8711 3.23 - 3.79: 14607 3.79 - 4.34: 19637 4.34 - 4.90: 33159 Nonbonded interactions: 76327 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.123 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.192 2.440 nonbonded pdb=" OG1 THR R 242 " pdb=" OE1 GLN R 252 " model vdw 2.201 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.203 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR N 176 " model vdw 2.216 2.440 ... (remaining 76322 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: 0.660 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: 3.950 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.000 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.006 0.148 9294 Z= 0.376 Angle : 1.018 34.457 12599 Z= 0.556 Chirality : 0.053 0.290 1444 Planarity : 0.004 0.053 1590 Dihedral : 16.622 147.684 3335 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.21 % Allowed : 22.94 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.34 (0.25), residues: 1140 helix: 1.23 (0.28), residues: 366 sheet: -0.28 (0.31), residues: 275 loop : -0.09 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 104 HIS 0.003 0.001 HIS R 142 PHE 0.025 0.002 PHE R 267 TYR 0.015 0.001 TYR N 191 ARG 0.009 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.2986 time to fit residues: 50.7318 Evaluate side-chains 119 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 313 ASN B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9294 Z= 0.204 Angle : 0.523 6.512 12599 Z= 0.271 Chirality : 0.042 0.140 1444 Planarity : 0.004 0.051 1590 Dihedral : 10.039 151.945 1321 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 22.12 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.57 (0.25), residues: 1140 helix: 1.42 (0.27), residues: 379 sheet: -0.13 (0.31), residues: 268 loop : -0.03 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS N 35 PHE 0.018 0.001 PHE R 51 TYR 0.010 0.001 TYR N 191 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8038 (pp) REVERT: B 219 ARG cc_start: 0.7647 (mtp85) cc_final: 0.7368 (mtp85) outliers start: 28 outliers final: 14 residues processed: 142 average time/residue: 0.2751 time to fit residues: 51.7181 Evaluate side-chains 141 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9294 Z= 0.263 Angle : 0.534 6.422 12599 Z= 0.276 Chirality : 0.042 0.139 1444 Planarity : 0.004 0.048 1590 Dihedral : 9.735 149.540 1321 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.60 % Allowed : 22.53 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.65 (0.25), residues: 1140 helix: 1.57 (0.27), residues: 378 sheet: -0.07 (0.32), residues: 268 loop : -0.05 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 104 HIS 0.003 0.001 HIS N 35 PHE 0.013 0.002 PHE R 51 TYR 0.009 0.001 TYR N 103 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 17 LYS cc_start: 0.7734 (mttt) cc_final: 0.7173 (mptt) REVERT: A 166 GLU cc_start: 0.7389 (tp30) cc_final: 0.7155 (tp30) REVERT: N 11 LEU cc_start: 0.7819 (tp) cc_final: 0.7359 (mm) REVERT: N 142 THR cc_start: 0.8544 (m) cc_final: 0.8325 (p) outliers start: 35 outliers final: 23 residues processed: 152 average time/residue: 0.2607 time to fit residues: 52.8009 Evaluate side-chains 147 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 119 ASN A 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9294 Z= 0.216 Angle : 0.521 7.998 12599 Z= 0.267 Chirality : 0.041 0.136 1444 Planarity : 0.004 0.047 1590 Dihedral : 9.460 144.288 1321 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.70 % Allowed : 23.35 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.70 (0.25), residues: 1140 helix: 1.69 (0.27), residues: 378 sheet: -0.05 (0.32), residues: 270 loop : -0.09 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 104 HIS 0.003 0.001 HIS N 35 PHE 0.016 0.001 PHE N 68 TYR 0.010 0.001 TYR N 191 ARG 0.004 0.000 ARG R 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7825 (pp) REVERT: A 17 LYS cc_start: 0.7737 (mttt) cc_final: 0.7139 (mptt) REVERT: A 166 GLU cc_start: 0.7459 (tp30) cc_final: 0.7182 (tp30) REVERT: N 11 LEU cc_start: 0.7794 (tp) cc_final: 0.7336 (mm) outliers start: 36 outliers final: 23 residues processed: 154 average time/residue: 0.2599 time to fit residues: 53.3108 Evaluate side-chains 146 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.0270 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9294 Z= 0.337 Angle : 0.577 7.651 12599 Z= 0.297 Chirality : 0.043 0.171 1444 Planarity : 0.004 0.048 1590 Dihedral : 9.316 138.549 1319 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.22 % Allowed : 24.18 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.59 (0.25), residues: 1140 helix: 1.61 (0.27), residues: 374 sheet: -0.11 (0.31), residues: 275 loop : -0.14 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 104 HIS 0.004 0.001 HIS N 35 PHE 0.019 0.002 PHE R 51 TYR 0.011 0.002 TYR R 321 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7763 (pp) REVERT: A 17 LYS cc_start: 0.7783 (mttt) cc_final: 0.7179 (mptt) REVERT: A 89 GLN cc_start: 0.7642 (mp-120) cc_final: 0.7432 (mp10) REVERT: A 166 GLU cc_start: 0.7501 (tp30) cc_final: 0.7257 (tp30) REVERT: N 11 LEU cc_start: 0.7833 (tp) cc_final: 0.7373 (mm) REVERT: N 18 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.7771 (tpt-90) outliers start: 41 outliers final: 31 residues processed: 155 average time/residue: 0.2486 time to fit residues: 51.7370 Evaluate side-chains 155 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9294 Z= 0.181 Angle : 0.512 7.691 12599 Z= 0.260 Chirality : 0.041 0.133 1444 Planarity : 0.003 0.048 1590 Dihedral : 8.961 129.581 1319 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.22 % Allowed : 24.28 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.72 (0.25), residues: 1140 helix: 1.77 (0.27), residues: 376 sheet: -0.06 (0.32), residues: 270 loop : -0.11 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS N 35 PHE 0.019 0.001 PHE R 51 TYR 0.011 0.001 TYR N 191 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 17 LYS cc_start: 0.7712 (mttt) cc_final: 0.7122 (mptt) REVERT: A 89 GLN cc_start: 0.7527 (mp-120) cc_final: 0.7326 (mp10) REVERT: A 166 GLU cc_start: 0.7495 (tp30) cc_final: 0.7262 (tp30) REVERT: A 245 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6887 (mp) REVERT: N 11 LEU cc_start: 0.7838 (tp) cc_final: 0.7370 (mm) REVERT: N 18 ARG cc_start: 0.8342 (tpp-160) cc_final: 0.7726 (tpt-90) outliers start: 41 outliers final: 31 residues processed: 154 average time/residue: 0.2553 time to fit residues: 52.2077 Evaluate side-chains 154 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 215 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0470 chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 0.0020 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9294 Z= 0.136 Angle : 0.495 8.942 12599 Z= 0.247 Chirality : 0.040 0.131 1444 Planarity : 0.003 0.047 1590 Dihedral : 8.495 118.959 1319 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.81 % Allowed : 24.69 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.86 (0.25), residues: 1140 helix: 1.90 (0.27), residues: 378 sheet: 0.01 (0.32), residues: 269 loop : -0.05 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS N 35 PHE 0.019 0.001 PHE R 51 TYR 0.011 0.001 TYR N 191 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7696 (mttt) cc_final: 0.7099 (mptt) REVERT: A 166 GLU cc_start: 0.7562 (tp30) cc_final: 0.7321 (tp30) REVERT: N 11 LEU cc_start: 0.7831 (tp) cc_final: 0.7360 (mm) REVERT: N 18 ARG cc_start: 0.8317 (tpp-160) cc_final: 0.7662 (tpt-90) REVERT: N 68 PHE cc_start: 0.7034 (m-80) cc_final: 0.6773 (m-80) outliers start: 37 outliers final: 27 residues processed: 154 average time/residue: 0.2619 time to fit residues: 53.6582 Evaluate side-chains 154 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9294 Z= 0.186 Angle : 0.518 7.706 12599 Z= 0.258 Chirality : 0.041 0.133 1444 Planarity : 0.003 0.047 1590 Dihedral : 8.393 118.353 1319 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.12 % Allowed : 23.97 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.86 (0.25), residues: 1140 helix: 1.91 (0.27), residues: 379 sheet: 0.02 (0.32), residues: 269 loop : -0.07 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 104 HIS 0.003 0.001 HIS N 35 PHE 0.017 0.001 PHE R 51 TYR 0.010 0.001 TYR N 191 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7686 (mttt) cc_final: 0.7088 (mptt) REVERT: A 166 GLU cc_start: 0.7579 (tp30) cc_final: 0.7333 (tp30) REVERT: N 11 LEU cc_start: 0.7829 (tp) cc_final: 0.7350 (mm) REVERT: N 18 ARG cc_start: 0.8318 (tpp-160) cc_final: 0.7661 (tpt-90) outliers start: 40 outliers final: 33 residues processed: 155 average time/residue: 0.2621 time to fit residues: 53.7617 Evaluate side-chains 159 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0770 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9294 Z= 0.256 Angle : 0.555 9.701 12599 Z= 0.278 Chirality : 0.042 0.161 1444 Planarity : 0.004 0.047 1590 Dihedral : 8.448 117.964 1319 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.12 % Allowed : 23.97 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.76 (0.25), residues: 1140 helix: 1.79 (0.27), residues: 378 sheet: 0.02 (0.32), residues: 272 loop : -0.12 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 104 HIS 0.004 0.001 HIS N 35 PHE 0.015 0.002 PHE N 68 TYR 0.009 0.001 TYR N 103 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7735 (mttt) cc_final: 0.7140 (mptt) REVERT: A 166 GLU cc_start: 0.7578 (tp30) cc_final: 0.7350 (tp30) REVERT: N 11 LEU cc_start: 0.7797 (tp) cc_final: 0.7278 (mm) REVERT: N 18 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7640 (tpt-90) outliers start: 40 outliers final: 37 residues processed: 153 average time/residue: 0.2500 time to fit residues: 51.2665 Evaluate side-chains 159 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.0060 chunk 75 optimal weight: 0.0040 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9294 Z= 0.137 Angle : 0.509 9.038 12599 Z= 0.251 Chirality : 0.040 0.137 1444 Planarity : 0.003 0.048 1590 Dihedral : 8.095 116.044 1319 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.98 % Allowed : 24.79 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.88 (0.25), residues: 1140 helix: 1.95 (0.27), residues: 378 sheet: 0.03 (0.32), residues: 269 loop : -0.09 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS B 54 PHE 0.017 0.001 PHE R 51 TYR 0.012 0.001 TYR N 191 ARG 0.006 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7238 (ptp) cc_final: 0.6930 (ptp) REVERT: A 17 LYS cc_start: 0.7672 (mttt) cc_final: 0.7075 (mptt) REVERT: A 199 ASP cc_start: 0.8076 (m-30) cc_final: 0.7760 (m-30) REVERT: N 11 LEU cc_start: 0.7764 (tp) cc_final: 0.7286 (mm) REVERT: N 18 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7586 (tpt-90) outliers start: 29 outliers final: 25 residues processed: 151 average time/residue: 0.2513 time to fit residues: 50.1727 Evaluate side-chains 153 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 79 optimal weight: 0.0170 chunk 5 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.167813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120410 restraints weight = 10664.637| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.66 r_work: 0.3260 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9294 Z= 0.137 Angle : 0.507 9.051 12599 Z= 0.250 Chirality : 0.040 0.140 1444 Planarity : 0.003 0.047 1590 Dihedral : 7.840 114.971 1319 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.57 % Allowed : 25.10 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.96 (0.25), residues: 1140 helix: 2.05 (0.27), residues: 378 sheet: 0.07 (0.32), residues: 269 loop : -0.05 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS N 35 PHE 0.017 0.001 PHE R 51 TYR 0.010 0.001 TYR N 191 ARG 0.008 0.000 ARG N 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.08 seconds wall clock time: 41 minutes 12.65 seconds (2472.65 seconds total)