Starting phenix.real_space_refine on Fri Sep 11 06:42:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.map" model { file = "/net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tko_10515/09_2026/6tko_10515.cif" } resolution = 3.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 C 5177 2.51 5 N 1358 2.21 5 O 1508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8085 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2241 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2684 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1529 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1606 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.17 Number of scatterers: 8085 At special positions: 0 Unit cell: (126.5, 106.7, 104.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 6 15.00 O 1508 8.00 N 1358 7.00 C 5177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.50 Conformation dependent library (CDL) restraints added in 393.6 milliseconds 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 16 sheets defined 27.9% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 44 through 69 removed outlier: 3.957A pdb=" N VAL A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 105 removed outlier: 3.535A pdb=" N LEU A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 110 through 144 removed outlier: 3.938A pdb=" N GLU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 4.221A pdb=" N SER A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 180 removed outlier: 4.237A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 216 through 242 Processing helix chain 'A' and resid 281 through 316 removed outlier: 3.708A pdb=" N PHE A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.696A pdb=" N VAL A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 344 removed outlier: 3.904A pdb=" N ASN A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Proline residue: A 340 - end of helix Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 280 through 284 removed outlier: 4.087A pdb=" N GLU B 283 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.542A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.685A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1361 through 1364 removed outlier: 3.670A pdb=" N ALA A1361 " --> pdb=" O LYS B 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.967A pdb=" N LEU B 166 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 146 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.967A pdb=" N LEU B 166 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 146 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.635A pdb=" N ALA B 201 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.635A pdb=" N ALA B 201 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.870A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.811A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA H 95 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR H 97 " --> pdb=" O THR H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.605A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.605A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.602A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA L 14 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.730A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.512A pdb=" N ASN L 139 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER L 175 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156 removed outlier: 4.589A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1143 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: 1.09 Time building geometry restraints manager: 0.72 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: 2531 1.34 - 1.46: 1273 1.46 - 1.57: 4417 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 8271 Sorted by residual: bond pdb=" OG1 TPO A1360 " pdb=" P TPO A1360 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" OG1 TPO A1359 " pdb=" P TPO A1359 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O2P SEP A1363 " pdb=" P SEP A1363 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O3P SEP A1363 " pdb=" P SEP A1363 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O3P SEP A1362 " pdb=" P SEP A1362 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.53e+01 ... (remaining 8266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 11191 2.34 - 4.69: 71 4.69 - 7.03: 10 7.03 - 9.37: 3 9.37 - 11.71: 4 Bond angle restraints: 11279 Sorted by residual: angle pdb=" CB SEP A1364 " pdb=" OG SEP A1364 " pdb=" P SEP A1364 " ideal model delta sigma weight residual 110.00 121.71 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB SEP A1363 " pdb=" OG SEP A1363 " pdb=" P SEP A1363 " ideal model delta sigma weight residual 110.00 120.85 -10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CB SEP A1357 " pdb=" OG SEP A1357 " pdb=" P SEP A1357 " ideal model delta sigma weight residual 110.00 120.57 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB SEP A1362 " pdb=" OG SEP A1362 " pdb=" P SEP A1362 " ideal model delta sigma weight residual 110.00 120.51 -10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" OG1 TPO A1359 " pdb=" P TPO A1359 " pdb=" O1P TPO A1359 " ideal model delta sigma weight residual 100.43 109.13 -8.70 3.00e+00 1.11e-01 8.41e+00 ... (remaining 11274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4585 17.44 - 34.89: 286 34.89 - 52.33: 50 52.33 - 69.77: 6 69.77 - 87.22: 9 Dihedral angle restraints: 4936 sinusoidal: 1851 harmonic: 3085 Sorted by residual: dihedral pdb=" CB CYS A 44 " pdb=" SG CYS A 44 " pdb=" SG CYS A 103 " pdb=" CB CYS A 103 " ideal model delta sinusoidal sigma weight residual 93.00 36.03 56.97 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CA ASP B 78 " pdb=" CB ASP B 78 " pdb=" CG ASP B 78 " pdb=" OD1 ASP B 78 " ideal model delta sinusoidal sigma weight residual -30.00 -82.26 52.26 1 2.00e+01 2.50e-03 9.31e+00 dihedral pdb=" CA ARG A 345 " pdb=" CB ARG A 345 " pdb=" CG ARG A 345 " pdb=" CD ARG A 345 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1136 0.055 - 0.109: 143 0.109 - 0.164: 28 0.164 - 0.218: 0 0.218 - 0.273: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" C12 H98 A2001 " pdb=" C11 H98 A2001 " pdb=" C13 H98 A2001 " pdb=" O4 H98 A2001 " both_signs ideal model delta sigma weight residual False -2.43 -2.70 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C2 H98 A2001 " pdb=" C1 H98 A2001 " pdb=" C3 H98 A2001 " pdb=" N1 H98 A2001 " both_signs ideal model delta sigma weight residual False 2.57 2.71 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1305 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 275 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.03e-01 pdb=" N PRO B 276 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 218 " 0.012 5.00e-02 4.00e+02 1.82e-02 5.28e-01 pdb=" N PRO A 219 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.012 5.00e-02 4.00e+02 1.79e-02 5.15e-01 pdb=" N PRO H 159 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.010 5.00e-02 4.00e+02 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 88 2.64 - 3.21: 7440 3.21 - 3.77: 12363 3.77 - 4.34: 17084 4.34 - 4.90: 28443 Nonbonded interactions: 65418 Sorted by model distance: nonbonded pdb=" OG SER B 13 " pdb=" OD1 ASN B 15 " model vdw 2.079 3.040 nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 102 " model vdw 2.096 3.040 nonbonded pdb=" O HIS L 190 " pdb=" NH1 ARG L 212 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR A 193 " pdb=" O VAL A 202 " model vdw 2.279 3.040 nonbonded pdb=" O PHE B 277 " pdb=" ND2 ASN B 281 " model vdw 2.285 3.120 ... (remaining 65413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 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: 0.820 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 0.107 8278 Z= 0.243 Angle : 0.509 11.713 11293 Z= 0.242 Chirality : 0.040 0.273 1308 Planarity : 0.002 0.021 1413 Dihedral : 12.087 87.216 2919 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.23 % Allowed : 7.58 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.24), residues: 1023 helix: -0.38 (0.29), residues: 255 sheet: -1.90 (0.25), residues: 333 loop : -1.36 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 165 TYR 0.004 0.000 TYR L 92 PHE 0.004 0.000 PHE A 147 TRP 0.002 0.000 TRP A 330 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.24 ( 8271) covalent geometry : angle 0.50922 / 0.24 (11279) SS BOND : bond 0.00042 / 0.03 ( 7) SS BOND : angle 0.18720 / 0.14 ( 14) hydrogen bonds : bond 0.20574 / 13.84 ( 392) hydrogen bonds : angle 7.75909 / 5.86 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.7881 (m-40) cc_final: 0.7569 (m-40) REVERT: A 121 ASP cc_start: 0.8282 (t0) cc_final: 0.8066 (t0) REVERT: A 154 THR cc_start: 0.8467 (m) cc_final: 0.8072 (p) REVERT: A 182 TRP cc_start: 0.7354 (p-90) cc_final: 0.6972 (p-90) REVERT: A 192 CYS cc_start: 0.4226 (t) cc_final: 0.3700 (t) REVERT: A 204 ASN cc_start: 0.7277 (p0) cc_final: 0.6898 (p0) REVERT: A 217 TYR cc_start: 0.7651 (m-80) cc_final: 0.7390 (m-80) REVERT: A 221 LEU cc_start: 0.8424 (tp) cc_final: 0.8158 (tt) REVERT: A 235 LYS cc_start: 0.7549 (mttt) cc_final: 0.7322 (mtpp) REVERT: A 325 PHE cc_start: 0.8508 (t80) cc_final: 0.8230 (t80) REVERT: A 339 ASN cc_start: 0.8419 (m-40) cc_final: 0.8104 (m110) REVERT: B 29 ASP cc_start: 0.7763 (t0) cc_final: 0.7501 (t0) REVERT: H 111 ASP cc_start: 0.7495 (m-30) cc_final: 0.6562 (m-30) REVERT: L 3 ILE cc_start: 0.7294 (mt) cc_final: 0.7026 (mp) REVERT: L 80 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7661 (mp10) REVERT: L 91 GLN cc_start: 0.8215 (pp30) cc_final: 0.7818 (pp30) REVERT: L 178 SER cc_start: 0.8134 (t) cc_final: 0.7860 (t) REVERT: L 195 CYS cc_start: 0.4880 (m) cc_final: 0.4225 (m) outliers start: 2 outliers final: 1 residues processed: 305 average time/residue: 0.0844 time to fit residues: 34.8677 Evaluate side-chains 195 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 GLN B 162 ASN H 31 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN L 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.173695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130170 restraints weight = 11516.369| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.67 r_work: 0.3512 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8278 Z= 0.171 Angle : 0.610 9.970 11293 Z= 0.307 Chirality : 0.043 0.183 1308 Planarity : 0.005 0.049 1413 Dihedral : 5.654 83.602 1152 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.27 % Allowed : 13.89 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.25), residues: 1023 helix: 1.28 (0.31), residues: 259 sheet: -1.19 (0.27), residues: 329 loop : -0.69 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 285 TYR 0.016 0.002 TYR L 141 PHE 0.021 0.002 PHE H 156 TRP 0.009 0.001 TRP A 181 HIS 0.003 0.001 HIS B 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8271) covalent geometry : angle 0.60831 / 0.31 (11279) SS BOND : bond 0.00451 / 0.17 ( 7) SS BOND : angle 1.40646 / 1.17 ( 14) hydrogen bonds : bond 0.03748 / 2.52 ( 392) hydrogen bonds : angle 5.59891 / 4.21 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8802 (tpp) cc_final: 0.8473 (mmm) REVERT: A 154 THR cc_start: 0.8327 (m) cc_final: 0.7890 (p) REVERT: A 192 CYS cc_start: 0.4424 (t) cc_final: 0.4184 (t) REVERT: A 221 LEU cc_start: 0.8438 (tp) cc_final: 0.8153 (tt) REVERT: A 235 LYS cc_start: 0.7768 (mttt) cc_final: 0.7385 (mtpp) REVERT: A 325 PHE cc_start: 0.8535 (t80) cc_final: 0.8326 (t80) REVERT: A 339 ASN cc_start: 0.8592 (m-40) cc_final: 0.8318 (m110) REVERT: B 346 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7459 (mt-10) REVERT: H 68 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8155 (ttpp) REVERT: H 83 TYR cc_start: 0.8128 (m-80) cc_final: 0.7860 (m-80) REVERT: H 120 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8545 (m) REVERT: H 220 LYS cc_start: 0.8792 (pptt) cc_final: 0.8311 (pptt) REVERT: L 25 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7537 (mtp-110) REVERT: L 71 ASP cc_start: 0.8236 (m-30) cc_final: 0.8030 (m-30) REVERT: L 91 GLN cc_start: 0.8676 (pp30) cc_final: 0.8304 (pp30) REVERT: L 109 ARG cc_start: 0.7902 (ptm160) cc_final: 0.7701 (ptm160) REVERT: L 146 LYS cc_start: 0.8754 (tptm) cc_final: 0.8550 (tttm) REVERT: L 150 LYS cc_start: 0.8338 (mttt) cc_final: 0.7938 (mmmt) REVERT: L 178 SER cc_start: 0.8180 (t) cc_final: 0.7815 (t) outliers start: 28 outliers final: 16 residues processed: 226 average time/residue: 0.0820 time to fit residues: 25.3981 Evaluate side-chains 198 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN B 30 HIS B 172 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.169203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124357 restraints weight = 11302.122| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.64 r_work: 0.3488 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8278 Z= 0.184 Angle : 0.604 7.616 11293 Z= 0.304 Chirality : 0.043 0.210 1308 Planarity : 0.004 0.031 1413 Dihedral : 5.781 82.531 1151 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.15 % Allowed : 15.52 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.26), residues: 1023 helix: 1.64 (0.31), residues: 259 sheet: -1.00 (0.28), residues: 328 loop : -0.43 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 236 TYR 0.015 0.002 TYR B 173 PHE 0.025 0.002 PHE H 156 TRP 0.008 0.001 TRP A 181 HIS 0.005 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 8271) covalent geometry : angle 0.60230 / 0.30 (11279) SS BOND : bond 0.00235 / 0.20 ( 7) SS BOND : angle 1.39342 / 1.12 ( 14) hydrogen bonds : bond 0.03508 / 2.41 ( 392) hydrogen bonds : angle 5.46644 / 4.07 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8944 (tpp) cc_final: 0.8474 (mmm) REVERT: A 154 THR cc_start: 0.8462 (m) cc_final: 0.8116 (m) REVERT: A 226 VAL cc_start: 0.7887 (p) cc_final: 0.7647 (p) REVERT: A 235 LYS cc_start: 0.7760 (mttt) cc_final: 0.7329 (mtpp) REVERT: A 323 TRP cc_start: 0.8344 (p-90) cc_final: 0.7873 (t60) REVERT: A 339 ASN cc_start: 0.8411 (m-40) cc_final: 0.8104 (m-40) REVERT: B 58 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8431 (t) REVERT: H 68 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8217 (ttpp) REVERT: H 83 TYR cc_start: 0.8201 (m-80) cc_final: 0.7959 (m-80) REVERT: H 119 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7226 (m) REVERT: L 25 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7609 (mtp-110) REVERT: L 71 ASP cc_start: 0.8183 (m-30) cc_final: 0.7979 (m-30) REVERT: L 91 GLN cc_start: 0.8801 (pp30) cc_final: 0.8353 (pp30) REVERT: L 109 ARG cc_start: 0.7952 (ptm160) cc_final: 0.7674 (ptm160) REVERT: L 150 LYS cc_start: 0.8268 (mttt) cc_final: 0.7800 (mmmt) REVERT: L 174 TYR cc_start: 0.8299 (m-80) cc_final: 0.7925 (m-80) REVERT: L 177 SER cc_start: 0.8569 (m) cc_final: 0.8047 (m) REVERT: L 191 LYS cc_start: 0.7838 (tptt) cc_final: 0.7603 (tptp) REVERT: L 196 GLU cc_start: 0.7865 (tt0) cc_final: 0.7419 (pt0) outliers start: 27 outliers final: 15 residues processed: 218 average time/residue: 0.0765 time to fit residues: 22.9852 Evaluate side-chains 198 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 68 optimal weight: 0.0570 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 172 GLN L 39 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.168401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123998 restraints weight = 11421.836| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.63 r_work: 0.3494 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8278 Z= 0.152 Angle : 0.594 8.056 11293 Z= 0.293 Chirality : 0.043 0.234 1308 Planarity : 0.004 0.033 1413 Dihedral : 5.831 82.947 1151 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.57 % Allowed : 18.90 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1023 helix: 1.66 (0.31), residues: 259 sheet: -0.85 (0.29), residues: 316 loop : -0.43 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 236 TYR 0.018 0.002 TYR L 141 PHE 0.023 0.002 PHE H 132 TRP 0.011 0.001 TRP A 182 HIS 0.006 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8271) covalent geometry : angle 0.59069 / 0.29 (11279) SS BOND : bond 0.00441 / 0.40 ( 7) SS BOND : angle 1.84290 / 1.32 ( 14) hydrogen bonds : bond 0.03262 / 2.22 ( 392) hydrogen bonds : angle 5.36100 / 3.96 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8978 (tpp) cc_final: 0.8436 (mmm) REVERT: A 154 THR cc_start: 0.8479 (m) cc_final: 0.8084 (m) REVERT: A 235 LYS cc_start: 0.7757 (mttt) cc_final: 0.7440 (mtpp) REVERT: A 323 TRP cc_start: 0.8345 (p-90) cc_final: 0.7963 (t60) REVERT: A 339 ASN cc_start: 0.8385 (m-40) cc_final: 0.8064 (m-40) REVERT: H 83 TYR cc_start: 0.8208 (m-80) cc_final: 0.7961 (m-80) REVERT: H 119 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.6954 (t) REVERT: L 25 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7612 (mtp-110) REVERT: L 71 ASP cc_start: 0.8167 (m-30) cc_final: 0.7930 (m-30) REVERT: L 91 GLN cc_start: 0.8711 (pp30) cc_final: 0.8354 (pp30) REVERT: L 109 ARG cc_start: 0.7900 (ptm160) cc_final: 0.7590 (ptm160) REVERT: L 150 LYS cc_start: 0.8228 (mttt) cc_final: 0.7539 (mmmt) REVERT: L 170 LYS cc_start: 0.8327 (tmmt) cc_final: 0.8008 (tmmt) REVERT: L 177 SER cc_start: 0.8583 (m) cc_final: 0.8120 (m) REVERT: L 196 GLU cc_start: 0.7922 (tt0) cc_final: 0.7474 (pt0) outliers start: 22 outliers final: 18 residues processed: 200 average time/residue: 0.0781 time to fit residues: 21.9999 Evaluate side-chains 194 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 87 optimal weight: 0.0570 chunk 89 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.169640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125599 restraints weight = 11287.909| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.60 r_work: 0.3449 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8278 Z= 0.139 Angle : 0.584 10.627 11293 Z= 0.289 Chirality : 0.042 0.163 1308 Planarity : 0.004 0.087 1413 Dihedral : 5.849 83.327 1151 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.98 % Allowed : 21.12 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1023 helix: 1.58 (0.31), residues: 263 sheet: -0.79 (0.29), residues: 316 loop : -0.42 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 19 TYR 0.019 0.001 TYR B 113 PHE 0.023 0.002 PHE H 132 TRP 0.016 0.001 TRP A 182 HIS 0.007 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8271) covalent geometry : angle 0.58148 / 0.29 (11279) SS BOND : bond 0.00291 / 0.15 ( 7) SS BOND : angle 1.74318 / 1.29 ( 14) hydrogen bonds : bond 0.03200 / 2.18 ( 392) hydrogen bonds : angle 5.29657 / 3.92 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8989 (tpp) cc_final: 0.8640 (mmm) REVERT: A 154 THR cc_start: 0.8500 (m) cc_final: 0.8084 (m) REVERT: A 235 LYS cc_start: 0.7795 (mttt) cc_final: 0.7470 (mtpp) REVERT: A 323 TRP cc_start: 0.8295 (p-90) cc_final: 0.7924 (t60) REVERT: A 339 ASN cc_start: 0.8378 (m-40) cc_final: 0.8062 (m-40) REVERT: B 78 ASP cc_start: 0.8149 (m-30) cc_final: 0.7852 (m-30) REVERT: H 83 TYR cc_start: 0.8157 (m-80) cc_final: 0.7903 (m-80) REVERT: H 119 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.6983 (t) REVERT: H 155 TYR cc_start: 0.8040 (p90) cc_final: 0.7663 (p90) REVERT: L 25 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7630 (mtp-110) REVERT: L 91 GLN cc_start: 0.8621 (pp30) cc_final: 0.8303 (pp30) REVERT: L 150 LYS cc_start: 0.8156 (mttt) cc_final: 0.7691 (mmmt) REVERT: L 170 LYS cc_start: 0.8316 (tmmt) cc_final: 0.7996 (tmmt) REVERT: L 177 SER cc_start: 0.8613 (m) cc_final: 0.8141 (m) REVERT: L 196 GLU cc_start: 0.7882 (tt0) cc_final: 0.7417 (pt0) outliers start: 17 outliers final: 12 residues processed: 199 average time/residue: 0.0781 time to fit residues: 21.9931 Evaluate side-chains 190 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.168278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123871 restraints weight = 11257.169| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.59 r_work: 0.3503 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8278 Z= 0.142 Angle : 0.591 9.386 11293 Z= 0.289 Chirality : 0.042 0.167 1308 Planarity : 0.004 0.076 1413 Dihedral : 5.854 83.086 1151 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.45 % Allowed : 21.24 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1023 helix: 1.61 (0.31), residues: 264 sheet: -0.76 (0.29), residues: 320 loop : -0.40 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 19 TYR 0.022 0.002 TYR B 113 PHE 0.025 0.002 PHE H 132 TRP 0.031 0.002 TRP A 107 HIS 0.007 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8271) covalent geometry : angle 0.58859 / 0.29 (11279) SS BOND : bond 0.00195 / 0.13 ( 7) SS BOND : angle 1.55661 / 1.15 ( 14) hydrogen bonds : bond 0.03188 / 2.18 ( 392) hydrogen bonds : angle 5.28024 / 3.90 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.9129 (tpp) cc_final: 0.8701 (mmm) REVERT: A 154 THR cc_start: 0.8463 (m) cc_final: 0.8113 (m) REVERT: A 235 LYS cc_start: 0.7751 (mttt) cc_final: 0.7426 (mtpp) REVERT: A 323 TRP cc_start: 0.8272 (p-90) cc_final: 0.7945 (t60) REVERT: A 339 ASN cc_start: 0.8358 (m-40) cc_final: 0.8056 (m-40) REVERT: B 78 ASP cc_start: 0.8209 (m-30) cc_final: 0.7897 (m-30) REVERT: H 119 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.6941 (t) REVERT: L 91 GLN cc_start: 0.8612 (pp30) cc_final: 0.8241 (pp30) REVERT: L 109 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7394 (ptm160) REVERT: L 150 LYS cc_start: 0.8285 (mttt) cc_final: 0.7817 (mmmt) REVERT: L 170 LYS cc_start: 0.8305 (tmmt) cc_final: 0.8048 (tmmt) REVERT: L 177 SER cc_start: 0.8701 (m) cc_final: 0.8230 (m) REVERT: L 196 GLU cc_start: 0.7841 (tt0) cc_final: 0.7411 (pt0) outliers start: 21 outliers final: 19 residues processed: 194 average time/residue: 0.0802 time to fit residues: 22.2392 Evaluate side-chains 197 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.168298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123723 restraints weight = 11406.899| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.62 r_work: 0.3438 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8278 Z= 0.138 Angle : 0.582 9.535 11293 Z= 0.287 Chirality : 0.042 0.172 1308 Planarity : 0.004 0.067 1413 Dihedral : 5.818 82.872 1151 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.80 % Allowed : 20.42 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1023 helix: 1.64 (0.31), residues: 264 sheet: -0.71 (0.29), residues: 332 loop : -0.38 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 25 TYR 0.022 0.002 TYR L 141 PHE 0.027 0.002 PHE H 132 TRP 0.029 0.002 TRP A 182 HIS 0.007 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8271) covalent geometry : angle 0.58011 / 0.29 (11279) SS BOND : bond 0.00205 / 0.12 ( 7) SS BOND : angle 1.45157 / 1.08 ( 14) hydrogen bonds : bond 0.03155 / 2.15 ( 392) hydrogen bonds : angle 5.25242 / 3.87 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 181 TRP cc_start: 0.7862 (m-90) cc_final: 0.7661 (m-90) REVERT: A 184 ASP cc_start: 0.6751 (t70) cc_final: 0.6325 (m-30) REVERT: A 193 TYR cc_start: 0.7790 (m-80) cc_final: 0.7540 (m-80) REVERT: A 235 LYS cc_start: 0.7791 (mttt) cc_final: 0.7499 (mtpp) REVERT: A 239 ARG cc_start: 0.6927 (mtp180) cc_final: 0.6652 (ptm160) REVERT: A 323 TRP cc_start: 0.8298 (p-90) cc_final: 0.7969 (t60) REVERT: A 339 ASN cc_start: 0.8360 (m-40) cc_final: 0.8032 (m-40) REVERT: B 78 ASP cc_start: 0.8188 (m-30) cc_final: 0.7949 (m-30) REVERT: H 83 TYR cc_start: 0.8224 (m-80) cc_final: 0.7875 (m-80) REVERT: H 119 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.6928 (t) REVERT: L 91 GLN cc_start: 0.8641 (pp30) cc_final: 0.8377 (pp30) REVERT: L 109 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7397 (ptm160) REVERT: L 150 LYS cc_start: 0.8286 (mttt) cc_final: 0.7796 (mmmt) REVERT: L 177 SER cc_start: 0.8786 (m) cc_final: 0.8309 (m) REVERT: L 196 GLU cc_start: 0.7882 (tt0) cc_final: 0.7422 (pt0) outliers start: 24 outliers final: 19 residues processed: 208 average time/residue: 0.0795 time to fit residues: 23.2416 Evaluate side-chains 196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 5 optimal weight: 0.0050 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.170167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125810 restraints weight = 11298.443| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.61 r_work: 0.3465 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8278 Z= 0.123 Angle : 0.611 8.954 11293 Z= 0.299 Chirality : 0.043 0.179 1308 Planarity : 0.004 0.054 1413 Dihedral : 5.827 83.120 1151 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.22 % Allowed : 21.94 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1023 helix: 1.71 (0.31), residues: 264 sheet: -0.65 (0.29), residues: 332 loop : -0.31 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 52 TYR 0.029 0.002 TYR L 141 PHE 0.028 0.002 PHE H 132 TRP 0.030 0.002 TRP A 182 HIS 0.010 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 8271) covalent geometry : angle 0.60967 / 0.30 (11279) SS BOND : bond 0.00124 / 0.08 ( 7) SS BOND : angle 1.30649 / 1.02 ( 14) hydrogen bonds : bond 0.03109 / 2.12 ( 392) hydrogen bonds : angle 5.25218 / 3.87 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 181 TRP cc_start: 0.7854 (m-90) cc_final: 0.7646 (m-90) REVERT: A 235 LYS cc_start: 0.7749 (mttt) cc_final: 0.7458 (mtpp) REVERT: A 239 ARG cc_start: 0.6824 (mtp180) cc_final: 0.6565 (ptm160) REVERT: A 323 TRP cc_start: 0.8287 (p-90) cc_final: 0.7948 (t60) REVERT: A 339 ASN cc_start: 0.8349 (m-40) cc_final: 0.8024 (m-40) REVERT: H 119 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.6828 (t) REVERT: L 91 GLN cc_start: 0.8589 (pp30) cc_final: 0.8253 (pp30) REVERT: L 101 GLN cc_start: 0.8164 (mm110) cc_final: 0.7821 (mm-40) REVERT: L 109 ARG cc_start: 0.7739 (ptm160) cc_final: 0.7253 (ptm160) REVERT: L 150 LYS cc_start: 0.8264 (mttt) cc_final: 0.7769 (mmmt) REVERT: L 177 SER cc_start: 0.8791 (m) cc_final: 0.8432 (m) REVERT: L 196 GLU cc_start: 0.7857 (tt0) cc_final: 0.7384 (pt0) outliers start: 19 outliers final: 16 residues processed: 199 average time/residue: 0.0757 time to fit residues: 21.6221 Evaluate side-chains 194 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 0.9980 chunk 61 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.167904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122754 restraints weight = 11217.380| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.58 r_work: 0.3426 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8278 Z= 0.158 Angle : 0.634 9.696 11293 Z= 0.312 Chirality : 0.043 0.182 1308 Planarity : 0.004 0.058 1413 Dihedral : 5.820 81.818 1151 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.45 % Allowed : 23.10 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1023 helix: 1.65 (0.32), residues: 264 sheet: -0.66 (0.29), residues: 333 loop : -0.25 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.032 0.002 TYR L 141 PHE 0.026 0.002 PHE H 132 TRP 0.032 0.002 TRP A 182 HIS 0.012 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8271) covalent geometry : angle 0.63222 / 0.31 (11279) SS BOND : bond 0.00211 / 0.12 ( 7) SS BOND : angle 1.33707 / 1.05 ( 14) hydrogen bonds : bond 0.03273 / 2.24 ( 392) hydrogen bonds : angle 5.32003 / 3.90 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 235 LYS cc_start: 0.7788 (mttt) cc_final: 0.7498 (mtpp) REVERT: A 239 ARG cc_start: 0.6870 (mtp180) cc_final: 0.6582 (ptm160) REVERT: A 323 TRP cc_start: 0.8201 (p-90) cc_final: 0.7883 (t60) REVERT: A 328 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8237 (t80) REVERT: A 339 ASN cc_start: 0.8366 (m-40) cc_final: 0.8048 (m-40) REVERT: B 78 ASP cc_start: 0.8089 (m-30) cc_final: 0.7771 (m-30) REVERT: B 85 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7845 (tp40) REVERT: H 9 GLU cc_start: 0.7292 (pm20) cc_final: 0.7077 (pm20) REVERT: H 68 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8454 (ttpp) REVERT: H 79 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7833 (pttt) REVERT: H 83 TYR cc_start: 0.7896 (m-80) cc_final: 0.7482 (m-80) REVERT: L 90 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: L 150 LYS cc_start: 0.8259 (mttt) cc_final: 0.7750 (mmmt) REVERT: L 177 SER cc_start: 0.8847 (m) cc_final: 0.8494 (p) REVERT: L 196 GLU cc_start: 0.7942 (tt0) cc_final: 0.7437 (pt0) outliers start: 21 outliers final: 17 residues processed: 198 average time/residue: 0.0799 time to fit residues: 22.4308 Evaluate side-chains 198 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121700 restraints weight = 11295.514| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.59 r_work: 0.3410 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8278 Z= 0.172 Angle : 0.658 11.455 11293 Z= 0.324 Chirality : 0.044 0.176 1308 Planarity : 0.005 0.060 1413 Dihedral : 5.871 81.293 1151 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.57 % Allowed : 23.34 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1023 helix: 1.63 (0.32), residues: 264 sheet: -0.67 (0.29), residues: 333 loop : -0.21 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 139 TYR 0.028 0.002 TYR L 141 PHE 0.025 0.002 PHE H 132 TRP 0.032 0.002 TRP A 182 HIS 0.011 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 8271) covalent geometry : angle 0.65672 / 0.32 (11279) SS BOND : bond 0.00238 / 0.14 ( 7) SS BOND : angle 1.39787 / 1.14 ( 14) hydrogen bonds : bond 0.03272 / 2.23 ( 392) hydrogen bonds : angle 5.34504 / 3.93 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.326 Fit side-chains REVERT: A 153 MET cc_start: 0.8968 (tpp) cc_final: 0.8327 (mmm) REVERT: A 235 LYS cc_start: 0.7787 (mttt) cc_final: 0.7493 (mtpp) REVERT: A 239 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6561 (ptm160) REVERT: A 323 TRP cc_start: 0.8082 (p-90) cc_final: 0.7789 (t60) REVERT: A 328 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8432 (t80) REVERT: A 339 ASN cc_start: 0.8378 (m-40) cc_final: 0.8080 (m-40) REVERT: B 78 ASP cc_start: 0.8101 (m-30) cc_final: 0.7785 (m-30) REVERT: H 79 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7802 (pttt) REVERT: H 83 TYR cc_start: 0.7942 (m-80) cc_final: 0.7488 (m-80) REVERT: L 101 GLN cc_start: 0.8164 (mm110) cc_final: 0.7844 (mm-40) REVERT: L 109 ARG cc_start: 0.7554 (ptm160) cc_final: 0.7025 (ptm160) REVERT: L 150 LYS cc_start: 0.8259 (mttt) cc_final: 0.7772 (mmmt) REVERT: L 177 SER cc_start: 0.8869 (m) cc_final: 0.8507 (p) REVERT: L 196 GLU cc_start: 0.7907 (tt0) cc_final: 0.7377 (pt0) outliers start: 22 outliers final: 19 residues processed: 193 average time/residue: 0.0757 time to fit residues: 20.9149 Evaluate side-chains 196 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 0.0470 chunk 74 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 GLN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121169 restraints weight = 11349.838| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.64 r_work: 0.3404 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8278 Z= 0.170 Angle : 0.661 11.644 11293 Z= 0.323 Chirality : 0.043 0.184 1308 Planarity : 0.005 0.057 1413 Dihedral : 5.852 81.043 1151 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.45 % Allowed : 23.92 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 1023 helix: 1.57 (0.32), residues: 264 sheet: -0.66 (0.29), residues: 333 loop : -0.17 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 139 TYR 0.025 0.002 TYR L 141 PHE 0.020 0.002 PHE A 216 TRP 0.037 0.002 TRP A 182 HIS 0.011 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 8271) covalent geometry : angle 0.65984 / 0.32 (11279) SS BOND : bond 0.00234 / 0.14 ( 7) SS BOND : angle 1.36955 / 1.13 ( 14) hydrogen bonds : bond 0.03296 / 2.24 ( 392) hydrogen bonds : angle 5.36495 / 3.93 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.60 seconds wall clock time: 39 minutes 35.56 seconds (2375.56 seconds total)