Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 19:52:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs3_34984/04_2023/8hs3_34984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs3_34984/04_2023/8hs3_34984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs3_34984/04_2023/8hs3_34984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs3_34984/04_2023/8hs3_34984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs3_34984/04_2023/8hs3_34984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hs3_34984/04_2023/8hs3_34984.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 59 5.16 5 C 5223 2.51 5 N 1453 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8258 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1709 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1761 Classifications: {'peptide': 279} Incomplete info: {'backbone_only': 4, 'n_c_alpha_c_only': 44, 'truncation_to_alanine': 46} Link IDs: {'PTRANS': 14, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 50 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 561 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 180 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.32, per 1000 atoms: 0.64 Number of scatterers: 8258 At special positions: 0 Unit cell: (95.68, 115.648, 129.792, 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 59 16.00 O 1523 8.00 N 1453 7.00 C 5223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.922A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.771A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.390A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.531A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 232' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.585A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.819A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.999A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.543A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 42 Processing helix chain 'R' and resid 56 through 80 WARNING: missing atoms! removed outlier: 3.579A pdb=" N LEU R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 113 Proline residue: R 107 - end of helix removed outlier: 4.222A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 133 removed outlier: 3.892A pdb=" N LEU R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 153 removed outlier: 3.614A pdb=" N VAL R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 185 removed outlier: 3.530A pdb=" N SER R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 206 Processing helix chain 'R' and resid 206 through 224 Processing helix chain 'R' and resid 229 through 231 No H-bonds generated for 'chain 'R' and resid 229 through 231' Processing helix chain 'R' and resid 232 through 254 removed outlier: 3.572A pdb=" N ARG R 236 " --> pdb=" O GLY R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 4.100A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 288 removed outlier: 3.726A pdb=" N TYR R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 308 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.709A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.857A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.963A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.987A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.695A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.558A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.727A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.920A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.684A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.729A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.670A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.649A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.352A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.815A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.742A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1092 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: 2.32 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2716 1.34 - 1.46: 1986 1.46 - 1.58: 3626 1.58 - 1.70: 4 1.70 - 1.81: 83 Bond restraints: 8415 Sorted by residual: bond pdb=" CB PRO R 226 " pdb=" CG PRO R 226 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" CB PRO R 268 " pdb=" CG PRO R 268 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.38e+00 bond pdb=" CB PRO R 271 " pdb=" CG PRO R 271 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.57e+00 bond pdb=" CB PRO S 75 " pdb=" CG PRO S 75 " ideal model delta sigma weight residual 1.492 1.636 -0.144 5.00e-02 4.00e+02 8.31e+00 bond pdb=" CG PRO R 268 " pdb=" CD PRO R 268 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.62e+00 ... (remaining 8410 not shown) Histogram of bond angle deviations from ideal: 95.47 - 103.18: 65 103.18 - 110.89: 2875 110.89 - 118.59: 3689 118.59 - 126.30: 4624 126.30 - 134.01: 116 Bond angle restraints: 11369 Sorted by residual: angle pdb=" CA PRO R 268 " pdb=" N PRO R 268 " pdb=" CD PRO R 268 " ideal model delta sigma weight residual 112.00 95.47 16.53 1.40e+00 5.10e-01 1.39e+02 angle pdb=" CA PRO R 271 " pdb=" N PRO R 271 " pdb=" CD PRO R 271 " ideal model delta sigma weight residual 112.00 97.72 14.28 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 97.74 14.26 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PRO R 226 " pdb=" N PRO R 226 " pdb=" CD PRO R 226 " ideal model delta sigma weight residual 112.00 100.12 11.88 1.40e+00 5.10e-01 7.20e+01 angle pdb=" N PRO R 268 " pdb=" CD PRO R 268 " pdb=" CG PRO R 268 " ideal model delta sigma weight residual 103.20 95.71 7.49 1.50e+00 4.44e-01 2.49e+01 ... (remaining 11364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4174 16.75 - 33.49: 557 33.49 - 50.24: 183 50.24 - 66.99: 24 66.99 - 83.74: 10 Dihedral angle restraints: 4948 sinusoidal: 1793 harmonic: 3155 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 165.29 -72.29 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CA SER B 334 " pdb=" C SER B 334 " pdb=" N PHE B 335 " pdb=" CA PHE B 335 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1054 0.056 - 0.112: 220 0.112 - 0.168: 17 0.168 - 0.224: 4 0.224 - 0.280: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA PRO R 271 " pdb=" N PRO R 271 " pdb=" C PRO R 271 " pdb=" CB PRO R 271 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA THR R 255 " pdb=" N THR R 255 " pdb=" C THR R 255 " pdb=" CB THR R 255 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1293 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP R 267 " -0.126 5.00e-02 4.00e+02 1.75e-01 4.87e+01 pdb=" N PRO R 268 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO R 268 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO R 268 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.099 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO S 75 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 270 " -0.074 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO R 271 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO R 271 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 271 " -0.056 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 212 2.69 - 3.24: 7695 3.24 - 3.80: 13427 3.80 - 4.35: 16816 4.35 - 4.90: 29017 Nonbonded interactions: 67167 Sorted by model distance: nonbonded pdb=" ND1 HIS R 126 " pdb=" NE2 HIS R 126 " model vdw 2.141 2.560 nonbonded pdb=" O MET A 18 " pdb=" ND2 ASN A 22 " model vdw 2.200 2.520 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASN R 133 " pdb=" OG SER R 286 " model vdw 2.277 2.440 ... (remaining 67162 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: 0.750 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: 4.420 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.290 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.171 8415 Z= 0.281 Angle : 0.751 16.527 11369 Z= 0.407 Chirality : 0.045 0.280 1296 Planarity : 0.009 0.175 1437 Dihedral : 16.983 83.736 2936 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.36 % 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: -1.38 (0.25), residues: 1106 helix: 0.18 (0.27), residues: 349 sheet: -1.39 (0.31), residues: 272 loop : -1.34 (0.28), residues: 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.965 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 115 average time/residue: 0.2030 time to fit residues: 32.6943 Evaluate side-chains 111 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0893 time to fit residues: 1.8641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 8415 Z= 0.308 Angle : 0.577 12.334 11369 Z= 0.303 Chirality : 0.044 0.186 1296 Planarity : 0.005 0.084 1437 Dihedral : 4.513 22.325 1203 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1106 helix: 0.80 (0.28), residues: 356 sheet: -1.33 (0.30), residues: 267 loop : -1.09 (0.28), residues: 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 0.985 Fit side-chains outliers start: 38 outliers final: 29 residues processed: 145 average time/residue: 0.1908 time to fit residues: 38.9369 Evaluate side-chains 140 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0761 time to fit residues: 5.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 40.0000 chunk 67 optimal weight: 40.0000 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 40.0000 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8415 Z= 0.212 Angle : 0.524 10.983 11369 Z= 0.274 Chirality : 0.042 0.168 1296 Planarity : 0.005 0.059 1437 Dihedral : 4.343 34.163 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1106 helix: 1.18 (0.28), residues: 354 sheet: -1.32 (0.29), residues: 292 loop : -1.02 (0.30), residues: 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.929 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 131 average time/residue: 0.1856 time to fit residues: 34.6138 Evaluate side-chains 119 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0847 time to fit residues: 2.6514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 40.0000 chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 8415 Z= 0.486 Angle : 0.667 11.661 11369 Z= 0.350 Chirality : 0.048 0.230 1296 Planarity : 0.005 0.059 1437 Dihedral : 4.861 36.664 1203 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 3.80 % 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: -0.92 (0.25), residues: 1106 helix: 0.95 (0.28), residues: 353 sheet: -1.47 (0.28), residues: 279 loop : -1.17 (0.29), residues: 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 26 residues processed: 133 average time/residue: 0.1914 time to fit residues: 36.3125 Evaluate side-chains 131 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.0842 time to fit residues: 5.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8415 Z= 0.190 Angle : 0.521 9.126 11369 Z= 0.269 Chirality : 0.042 0.169 1296 Planarity : 0.004 0.053 1437 Dihedral : 4.370 31.722 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1106 helix: 1.34 (0.29), residues: 352 sheet: -1.45 (0.28), residues: 288 loop : -1.01 (0.29), residues: 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.061 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 120 average time/residue: 0.2114 time to fit residues: 35.7174 Evaluate side-chains 114 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0880 time to fit residues: 2.3185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 55 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8415 Z= 0.295 Angle : 0.570 10.703 11369 Z= 0.294 Chirality : 0.044 0.184 1296 Planarity : 0.004 0.061 1437 Dihedral : 4.452 30.875 1203 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1106 helix: 1.25 (0.29), residues: 352 sheet: -1.43 (0.29), residues: 281 loop : -1.04 (0.29), residues: 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.923 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 119 average time/residue: 0.1854 time to fit residues: 31.7487 Evaluate side-chains 118 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0761 time to fit residues: 2.5767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.0570 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8415 Z= 0.166 Angle : 0.507 10.343 11369 Z= 0.261 Chirality : 0.042 0.156 1296 Planarity : 0.004 0.054 1437 Dihedral : 4.208 27.968 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.19 % 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: -0.48 (0.26), residues: 1106 helix: 1.41 (0.29), residues: 353 sheet: -1.25 (0.30), residues: 283 loop : -0.97 (0.29), residues: 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.925 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.1982 time to fit residues: 34.8960 Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0866 time to fit residues: 2.2878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 8415 Z= 0.314 Angle : 0.586 11.003 11369 Z= 0.303 Chirality : 0.045 0.181 1296 Planarity : 0.004 0.061 1437 Dihedral : 4.451 29.368 1203 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.19 % 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 (0.26), residues: 1106 helix: 1.26 (0.28), residues: 352 sheet: -1.32 (0.30), residues: 278 loop : -0.99 (0.29), residues: 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 116 average time/residue: 0.1919 time to fit residues: 31.7455 Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0794 time to fit residues: 2.1085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8415 Z= 0.146 Angle : 0.503 10.881 11369 Z= 0.259 Chirality : 0.041 0.154 1296 Planarity : 0.004 0.054 1437 Dihedral : 4.107 26.138 1203 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.07 % 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: -0.34 (0.26), residues: 1106 helix: 1.48 (0.29), residues: 352 sheet: -1.12 (0.30), residues: 281 loop : -0.87 (0.30), residues: 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.952 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 122 average time/residue: 0.2133 time to fit residues: 35.9652 Evaluate side-chains 113 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0802 time to fit residues: 1.7058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 8415 Z= 0.252 Angle : 0.555 10.471 11369 Z= 0.287 Chirality : 0.043 0.158 1296 Planarity : 0.004 0.062 1437 Dihedral : 4.268 27.876 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.71 % 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: -0.40 (0.26), residues: 1106 helix: 1.42 (0.29), residues: 352 sheet: -1.22 (0.30), residues: 286 loop : -0.85 (0.30), residues: 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.879 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 118 average time/residue: 0.1816 time to fit residues: 30.7845 Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0832 time to fit residues: 1.8207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 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 = 0.3986 r_free = 0.3986 target = 0.164545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119475 restraints weight = 9545.935| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.88 r_work: 0.3276 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8415 Z= 0.234 Angle : 0.549 10.379 11369 Z= 0.284 Chirality : 0.043 0.168 1296 Planarity : 0.004 0.053 1437 Dihedral : 4.276 27.318 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1106 helix: 1.39 (0.29), residues: 353 sheet: -1.23 (0.30), residues: 286 loop : -0.83 (0.30), residues: 467 =============================================================================== Job complete usr+sys time: 1913.60 seconds wall clock time: 35 minutes 39.45 seconds (2139.45 seconds total)