Starting phenix.real_space_refine on Wed Feb 14 14:44:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnk_34914/02_2024/8hnk_34914_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnk_34914/02_2024/8hnk_34914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnk_34914/02_2024/8hnk_34914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnk_34914/02_2024/8hnk_34914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnk_34914/02_2024/8hnk_34914_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnk_34914/02_2024/8hnk_34914_updated.pdb" } resolution = 3.01 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= 1.000 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 70 5.16 5 C 6050 2.51 5 N 1635 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 220": "OE1" <-> "OE2" Residue "S PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9492 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "R" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2316 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain: "L" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.58, per 1000 atoms: 0.59 Number of scatterers: 9492 At special positions: 0 Unit cell: (94.35, 121.55, 147.05, 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 70 16.00 O 1737 8.00 N 1635 7.00 C 6050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 290 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 36 " distance=2.03 Simple disulfide: pdb=" SG CYS L 11 " - pdb=" SG CYS L 53 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 3.78 Conformation dependent library (CDL) restraints added in 1.9 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 14 sheets defined 34.2% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 Processing helix chain 'A' and resid 46 through 52 removed outlier: 4.728A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.390A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.292A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 removed outlier: 4.453A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.588A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 22 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 46 through 80 Proline residue: R 57 - end of helix Processing helix chain 'R' and resid 87 through 114 Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 122 through 153 Processing helix chain 'R' and resid 156 through 162 Processing helix chain 'R' and resid 167 through 189 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 209 through 244 removed outlier: 5.748A pdb=" N LEU R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 250 through 283 Proline residue: R 270 - end of helix Processing helix chain 'R' and resid 290 through 318 Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 323 through 333 Processing helix chain 'L' and resid 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 59 through 71 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.521A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.941A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.029A 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: 6.903A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.953A 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: 6.831A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.932A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.678A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.598A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.702A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 191 through 195 removed outlier: 4.171A pdb=" N ALA R 200 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 27 through 30 Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.607A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.641A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 155 through 160 448 hydrogen bonds defined for protein. 1287 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: 2.67 Time building geometry restraints manager: 4.10 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: 3071 1.34 - 1.46: 2206 1.46 - 1.58: 4309 1.58 - 1.70: 1 1.70 - 1.82: 99 Bond restraints: 9686 Sorted by residual: bond pdb=" N ASP R 282 " pdb=" CA ASP R 282 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.35e+00 bond pdb=" CB PRO S 148 " pdb=" CG PRO S 148 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.21e+00 bond pdb=" N ARG L 6 " pdb=" CA ARG L 6 " ideal model delta sigma weight residual 1.455 1.473 -0.019 1.27e-02 6.20e+03 2.16e+00 bond pdb=" CB CYS B 114 " pdb=" SG CYS B 114 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" C3 CLR R 601 " pdb=" O1 CLR R 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 9681 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 158 105.83 - 112.88: 5280 112.88 - 119.94: 3157 119.94 - 126.99: 4415 126.99 - 134.05: 109 Bond angle restraints: 13119 Sorted by residual: angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 107.10 6.80 1.80e+00 3.09e-01 1.43e+01 angle pdb=" C LYS L 46 " pdb=" N GLU L 47 " pdb=" CA GLU L 47 " ideal model delta sigma weight residual 122.61 126.75 -4.14 1.56e+00 4.11e-01 7.05e+00 angle pdb=" C MET L 30 " pdb=" N TYR L 31 " pdb=" CA TYR L 31 " ideal model delta sigma weight residual 121.03 125.15 -4.12 1.60e+00 3.91e-01 6.65e+00 angle pdb=" CA ARG L 6 " pdb=" C ARG L 6 " pdb=" O ARG L 6 " ideal model delta sigma weight residual 121.33 118.56 2.77 1.08e+00 8.57e-01 6.57e+00 angle pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" C TYR S 235 " ideal model delta sigma weight residual 109.81 115.21 -5.40 2.21e+00 2.05e-01 5.98e+00 ... (remaining 13114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5333 17.93 - 35.86: 461 35.86 - 53.79: 79 53.79 - 71.72: 12 71.72 - 89.65: 5 Dihedral angle restraints: 5890 sinusoidal: 2392 harmonic: 3498 Sorted by residual: dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 290 " pdb=" CB CYS R 290 " ideal model delta sinusoidal sigma weight residual 93.00 172.22 -79.22 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1112 0.044 - 0.088: 289 0.088 - 0.132: 88 0.132 - 0.176: 7 0.176 - 0.220: 3 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CA ILE L 29 " pdb=" N ILE L 29 " pdb=" C ILE L 29 " pdb=" CB ILE L 29 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA LEU R 56 " pdb=" N LEU R 56 " pdb=" C LEU R 56 " pdb=" CB LEU R 56 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 1496 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO S 75 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO S 236 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " 0.025 2.00e-02 2.50e+03 1.52e-02 4.64e+00 pdb=" CG TYR S 235 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " 0.005 2.00e-02 2.50e+03 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 424 2.72 - 3.27: 9357 3.27 - 3.81: 14961 3.81 - 4.36: 18709 4.36 - 4.90: 33078 Nonbonded interactions: 76529 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.176 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.220 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.262 2.440 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.265 2.520 ... (remaining 76524 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.910 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.030 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.004 0.090 9686 Z= 0.244 Angle : 0.609 8.121 13119 Z= 0.341 Chirality : 0.044 0.220 1499 Planarity : 0.004 0.063 1651 Dihedral : 13.488 89.649 3614 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1192 helix: 1.50 (0.26), residues: 407 sheet: 0.10 (0.31), residues: 287 loop : -1.05 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 237 PHE 0.015 0.001 PHE R 207 TYR 0.034 0.002 TYR S 235 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.107 Fit side-chains REVERT: R 331 MET cc_start: 0.7491 (ttm) cc_final: 0.7207 (tmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2580 time to fit residues: 51.9197 Evaluate side-chains 129 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.0770 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9686 Z= 0.158 Angle : 0.535 7.348 13119 Z= 0.275 Chirality : 0.042 0.203 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.366 56.987 1441 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.88 % Allowed : 7.80 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1192 helix: 1.81 (0.26), residues: 407 sheet: 0.20 (0.30), residues: 293 loop : -1.01 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.015 0.001 PHE R 47 TYR 0.030 0.001 TYR S 235 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.020 Fit side-chains REVERT: G 51 LEU cc_start: 0.9093 (tp) cc_final: 0.8819 (tp) REVERT: R 68 LEU cc_start: 0.8730 (mm) cc_final: 0.8328 (mm) REVERT: S 6 GLU cc_start: 0.8185 (mp0) cc_final: 0.7599 (mt-10) outliers start: 9 outliers final: 6 residues processed: 135 average time/residue: 0.2699 time to fit residues: 48.7916 Evaluate side-chains 129 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9686 Z= 0.252 Angle : 0.557 9.509 13119 Z= 0.289 Chirality : 0.043 0.244 1499 Planarity : 0.004 0.059 1651 Dihedral : 5.290 59.791 1441 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.36 % Allowed : 9.94 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1192 helix: 1.80 (0.26), residues: 409 sheet: 0.33 (0.30), residues: 290 loop : -1.01 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE R 47 TYR 0.039 0.002 TYR S 235 ARG 0.004 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: G 51 LEU cc_start: 0.9108 (tp) cc_final: 0.8846 (tp) REVERT: R 68 LEU cc_start: 0.8769 (mm) cc_final: 0.8368 (mm) REVERT: S 6 GLU cc_start: 0.8314 (mp0) cc_final: 0.7591 (mt-10) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.2653 time to fit residues: 46.9714 Evaluate side-chains 133 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9686 Z= 0.246 Angle : 0.548 9.044 13119 Z= 0.283 Chirality : 0.043 0.250 1499 Planarity : 0.004 0.059 1651 Dihedral : 5.199 59.897 1441 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.95 % Allowed : 11.60 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1192 helix: 1.79 (0.26), residues: 410 sheet: 0.38 (0.30), residues: 291 loop : -1.00 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.038 0.002 TYR S 235 ARG 0.002 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8308 (mmp80) cc_final: 0.8023 (mmt-90) REVERT: G 51 LEU cc_start: 0.9104 (tp) cc_final: 0.8843 (tp) REVERT: R 68 LEU cc_start: 0.8780 (mm) cc_final: 0.8364 (mm) REVERT: S 220 GLU cc_start: 0.7743 (mp0) cc_final: 0.7241 (mp0) REVERT: S 235 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6717 (t80) outliers start: 20 outliers final: 15 residues processed: 141 average time/residue: 0.2549 time to fit residues: 48.2619 Evaluate side-chains 138 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9686 Z= 0.197 Angle : 0.518 8.237 13119 Z= 0.270 Chirality : 0.042 0.225 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.114 59.758 1441 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.85 % Allowed : 12.67 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1192 helix: 1.88 (0.26), residues: 410 sheet: 0.40 (0.30), residues: 292 loop : -1.00 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.014 0.001 PHE R 47 TYR 0.032 0.001 TYR S 235 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.117 Fit side-chains REVERT: G 51 LEU cc_start: 0.9115 (tp) cc_final: 0.8843 (tp) REVERT: R 68 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8379 (mm) REVERT: S 3 GLN cc_start: 0.8333 (pt0) cc_final: 0.8054 (pt0) REVERT: S 201 ASP cc_start: 0.8008 (t70) cc_final: 0.7768 (t0) REVERT: S 220 GLU cc_start: 0.7807 (mp0) cc_final: 0.7291 (mp0) REVERT: S 235 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6677 (t80) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.2599 time to fit residues: 46.6226 Evaluate side-chains 136 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9686 Z= 0.283 Angle : 0.565 9.587 13119 Z= 0.292 Chirality : 0.043 0.262 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.228 60.456 1441 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.14 % Allowed : 13.16 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1192 helix: 1.78 (0.26), residues: 410 sheet: 0.47 (0.30), residues: 289 loop : -1.01 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 47 TYR 0.042 0.002 TYR S 235 ARG 0.003 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.048 Fit side-chains REVERT: R 68 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8346 (mm) REVERT: S 3 GLN cc_start: 0.8347 (pt0) cc_final: 0.8075 (pt0) REVERT: S 235 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6881 (t80) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 0.2475 time to fit residues: 46.7651 Evaluate side-chains 138 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9686 Z= 0.162 Angle : 0.516 9.053 13119 Z= 0.267 Chirality : 0.041 0.205 1499 Planarity : 0.003 0.057 1651 Dihedral : 5.055 59.180 1441 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.24 % Allowed : 14.04 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1192 helix: 1.93 (0.26), residues: 410 sheet: 0.51 (0.31), residues: 284 loop : -1.00 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS R 272 PHE 0.016 0.001 PHE R 47 TYR 0.028 0.001 TYR S 235 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.067 Fit side-chains REVERT: G 51 LEU cc_start: 0.9099 (tp) cc_final: 0.8822 (tp) REVERT: R 68 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8367 (mm) REVERT: R 281 MET cc_start: 0.6539 (tmm) cc_final: 0.6312 (tmm) REVERT: S 3 GLN cc_start: 0.8247 (pt0) cc_final: 0.7977 (pt0) REVERT: S 234 GLU cc_start: 0.7289 (mp0) cc_final: 0.7087 (mp0) REVERT: S 235 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6451 (t80) outliers start: 23 outliers final: 15 residues processed: 136 average time/residue: 0.2346 time to fit residues: 43.9495 Evaluate side-chains 134 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9686 Z= 0.210 Angle : 0.536 8.972 13119 Z= 0.274 Chirality : 0.042 0.226 1499 Planarity : 0.004 0.057 1651 Dihedral : 5.057 59.084 1441 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.24 % Allowed : 13.84 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1192 helix: 1.89 (0.26), residues: 410 sheet: 0.54 (0.31), residues: 290 loop : -0.97 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.001 PHE R 47 TYR 0.035 0.002 TYR S 235 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.072 Fit side-chains REVERT: G 51 LEU cc_start: 0.9107 (tp) cc_final: 0.8848 (tp) REVERT: R 68 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8386 (mm) REVERT: R 281 MET cc_start: 0.6567 (tmm) cc_final: 0.6331 (tmm) REVERT: S 3 GLN cc_start: 0.8243 (pt0) cc_final: 0.7976 (pt0) REVERT: S 234 GLU cc_start: 0.7397 (mp0) cc_final: 0.7191 (mp0) REVERT: S 235 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6662 (t80) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 0.2291 time to fit residues: 43.6422 Evaluate side-chains 135 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9686 Z= 0.235 Angle : 0.565 12.762 13119 Z= 0.286 Chirality : 0.043 0.235 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.093 58.678 1441 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.85 % Allowed : 14.04 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1192 helix: 1.87 (0.26), residues: 410 sheet: 0.53 (0.31), residues: 284 loop : -0.97 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE R 47 TYR 0.037 0.002 TYR S 235 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.091 Fit side-chains REVERT: G 51 LEU cc_start: 0.9114 (tp) cc_final: 0.8852 (tp) REVERT: R 68 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8362 (mm) REVERT: R 281 MET cc_start: 0.6573 (tmm) cc_final: 0.6337 (tmm) REVERT: S 3 GLN cc_start: 0.8266 (pt0) cc_final: 0.8002 (pt0) REVERT: S 235 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6700 (t80) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.2289 time to fit residues: 42.3056 Evaluate side-chains 133 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9686 Z= 0.265 Angle : 0.584 12.706 13119 Z= 0.295 Chirality : 0.043 0.252 1499 Planarity : 0.004 0.058 1651 Dihedral : 5.164 59.697 1441 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.75 % Allowed : 14.23 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1192 helix: 1.82 (0.26), residues: 410 sheet: 0.47 (0.31), residues: 286 loop : -1.02 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.001 PHE R 47 TYR 0.039 0.002 TYR S 235 ARG 0.002 0.000 ARG S 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.121 Fit side-chains REVERT: A 21 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7124 (ptp-110) REVERT: G 51 LEU cc_start: 0.9126 (tp) cc_final: 0.8868 (tp) REVERT: R 68 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8342 (mm) REVERT: R 281 MET cc_start: 0.6636 (tmm) cc_final: 0.6386 (tmm) REVERT: S 3 GLN cc_start: 0.8343 (pt0) cc_final: 0.8076 (pt0) REVERT: S 235 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6800 (t80) outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 0.2401 time to fit residues: 42.6024 Evaluate side-chains 138 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** 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 = 0.3928 r_free = 0.3928 target = 0.141818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100163 restraints weight = 13729.431| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.30 r_work: 0.3094 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9686 Z= 0.170 Angle : 0.537 12.323 13119 Z= 0.270 Chirality : 0.041 0.211 1499 Planarity : 0.003 0.057 1651 Dihedral : 5.008 58.681 1441 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.56 % Allowed : 14.72 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1192 helix: 1.92 (0.26), residues: 411 sheet: 0.60 (0.31), residues: 283 loop : -0.95 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS R 237 PHE 0.019 0.001 PHE R 47 TYR 0.029 0.001 TYR S 235 ARG 0.002 0.000 ARG S 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.00 seconds wall clock time: 45 minutes 24.89 seconds (2724.89 seconds total)