Starting phenix.real_space_refine on Wed Feb 12 05:18:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9c_33071/02_2025/7x9c_33071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9c_33071/02_2025/7x9c_33071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x9c_33071/02_2025/7x9c_33071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9c_33071/02_2025/7x9c_33071.map" model { file = "/net/cci-nas-00/data/ceres_data/7x9c_33071/02_2025/7x9c_33071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9c_33071/02_2025/7x9c_33071.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 139 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 4615 2.51 5 N 1240 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7219 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2358 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1691 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2503 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 383 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 284 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 30} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 4.62, per 1000 atoms: 0.64 Number of scatterers: 7219 At special positions: 0 Unit cell: (123.31, 119.13, 84.645, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1302 8.00 N 1240 7.00 C 4615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 201 " 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: 1.69 Conformation dependent library (CDL) restraints added in 938.5 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 47.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'R' and resid 38 through 68 removed outlier: 3.955A pdb=" N VAL R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 103 removed outlier: 3.908A pdb=" N LEU R 78 " --> pdb=" O ASN R 74 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 110 through 144 Processing helix chain 'R' and resid 152 through 172 Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.612A pdb=" N ALA R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.898A pdb=" N ILE R 213 " --> pdb=" O HIS R 209 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR R 214 " --> pdb=" O HIS R 210 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 248 removed outlier: 3.580A pdb=" N VAL R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 277 Processing helix chain 'R' and resid 278 through 291 removed outlier: 3.746A pdb=" N HIS R 282 " --> pdb=" O TRP R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 313 Processing helix chain 'R' and resid 313 through 323 Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 326 through 330 removed outlier: 3.671A pdb=" N LYS R 330 " --> pdb=" O THR R 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 341 removed outlier: 3.663A pdb=" N ALA R 335 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL R 337 " --> pdb=" O ILE R 333 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.628A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.080A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.822A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.203A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.634A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.515A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.786A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.653A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.841A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 10 through 20 removed outlier: 3.812A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.575A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'P' and resid 13 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.885A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.470A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.715A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.890A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.824A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 7.105A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 7.096A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 371 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1161 1.31 - 1.43: 1987 1.43 - 1.56: 4130 1.56 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 7366 Sorted by residual: bond pdb=" C TYC P 36 " pdb=" NXT TYC P 36 " ideal model delta sigma weight residual 1.340 1.449 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CA LYS R 190 " pdb=" C LYS R 190 " ideal model delta sigma weight residual 1.522 1.583 -0.060 1.20e-02 6.94e+03 2.54e+01 bond pdb=" N LEU R 192 " pdb=" CA LEU R 192 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.20e+00 bond pdb=" N GLN R 121 " pdb=" CA GLN R 121 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.28e+00 bond pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 1.350 1.399 -0.049 2.00e-02 2.50e+03 6.09e+00 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9866 1.68 - 3.36: 122 3.36 - 5.03: 21 5.03 - 6.71: 5 6.71 - 8.39: 1 Bond angle restraints: 10015 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.46 4.01 1.01e+00 9.80e-01 1.58e+01 angle pdb=" C GLN R 121 " pdb=" CA GLN R 121 " pdb=" CB GLN R 121 " ideal model delta sigma weight residual 110.85 115.85 -5.00 1.70e+00 3.46e-01 8.65e+00 angle pdb=" C ILE R 144 " pdb=" N ASN R 145 " pdb=" CA ASN R 145 " ideal model delta sigma weight residual 121.80 128.47 -6.67 2.44e+00 1.68e-01 7.48e+00 angle pdb=" CA LEU R 172 " pdb=" CB LEU R 172 " pdb=" CG LEU R 172 " ideal model delta sigma weight residual 116.30 124.69 -8.39 3.50e+00 8.16e-02 5.75e+00 angle pdb=" CA GLN R 121 " pdb=" C GLN R 121 " pdb=" O GLN R 121 " ideal model delta sigma weight residual 120.42 117.91 2.51 1.06e+00 8.90e-01 5.61e+00 ... (remaining 10010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 4097 15.95 - 31.89: 212 31.89 - 47.84: 46 47.84 - 63.78: 8 63.78 - 79.73: 1 Dihedral angle restraints: 4364 sinusoidal: 1602 harmonic: 2762 Sorted by residual: dihedral pdb=" CA TYR B 85 " pdb=" C TYR B 85 " pdb=" N THR B 86 " pdb=" CA THR B 86 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 dihedral pdb=" C GLN R 121 " pdb=" N GLN R 121 " pdb=" CA GLN R 121 " pdb=" CB GLN R 121 " ideal model delta harmonic sigma weight residual -122.60 -130.21 7.61 0 2.50e+00 1.60e-01 9.27e+00 dihedral pdb=" CB GLU R 181 " pdb=" CG GLU R 181 " pdb=" CD GLU R 181 " pdb=" OE1 GLU R 181 " ideal model delta sinusoidal sigma weight residual 0.00 79.73 -79.73 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 4361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 848 0.037 - 0.073: 257 0.073 - 0.110: 61 0.110 - 0.147: 15 0.147 - 0.183: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA GLN R 121 " pdb=" N GLN R 121 " pdb=" C GLN R 121 " pdb=" CB GLN R 121 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA HIS R 188 " pdb=" N HIS R 188 " pdb=" C HIS R 188 " pdb=" CB HIS R 188 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1179 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 225 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO R 226 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 172 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO R 173 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 173 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 173 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO B 194 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.015 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 734 2.75 - 3.28: 7402 3.28 - 3.82: 12388 3.82 - 4.36: 14451 4.36 - 4.90: 24900 Nonbonded interactions: 59875 Sorted by model distance: nonbonded pdb=" OH TYR R 48 " pdb=" O LEU R 305 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OE1 GLU A 298 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR R 52 " pdb=" OE1 GLN R 95 " model vdw 2.329 3.040 ... (remaining 59870 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.003 0.109 7366 Z= 0.197 Angle : 0.510 8.390 10015 Z= 0.287 Chirality : 0.038 0.183 1182 Planarity : 0.003 0.031 1260 Dihedral : 10.402 79.725 2563 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.24), residues: 928 helix: -1.03 (0.24), residues: 392 sheet: -1.64 (0.36), residues: 183 loop : -2.20 (0.28), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 205 HIS 0.005 0.000 HIS R 188 PHE 0.010 0.001 PHE B 253 TYR 0.014 0.001 TYR R 48 ARG 0.001 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: R 109 PHE cc_start: 0.7654 (m-80) cc_final: 0.7426 (m-80) REVERT: R 115 LYS cc_start: 0.5513 (mtpp) cc_final: 0.5241 (mmpt) REVERT: A 35 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7903 (mtmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.9074 time to fit residues: 155.8760 Evaluate side-chains 112 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 306 GLN A 322 HIS B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.179291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132848 restraints weight = 8009.529| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.53 r_work: 0.3470 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7366 Z= 0.222 Angle : 0.582 9.128 10015 Z= 0.299 Chirality : 0.041 0.140 1182 Planarity : 0.003 0.028 1260 Dihedral : 5.247 59.245 1013 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.12 % Allowed : 11.42 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.26), residues: 928 helix: 0.18 (0.26), residues: 407 sheet: -1.33 (0.36), residues: 178 loop : -1.89 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS R 185 PHE 0.013 0.001 PHE A 274 TYR 0.014 0.002 TYR R 234 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: R 109 PHE cc_start: 0.7936 (m-80) cc_final: 0.7681 (m-80) REVERT: R 115 LYS cc_start: 0.5524 (mtpp) cc_final: 0.5020 (mmpt) REVERT: A 35 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8066 (mtmm) REVERT: A 198 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7258 (mpt) REVERT: A 258 TRP cc_start: 0.8069 (m-90) cc_final: 0.7728 (m-10) REVERT: B 259 GLN cc_start: 0.7416 (tp40) cc_final: 0.7068 (tp40) REVERT: B 262 MET cc_start: 0.7676 (ttm) cc_final: 0.7448 (mtm) outliers start: 16 outliers final: 8 residues processed: 134 average time/residue: 0.9491 time to fit residues: 136.3630 Evaluate side-chains 120 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 185 HIS ** R 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.172034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130367 restraints weight = 8122.927| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.43 r_work: 0.3360 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7366 Z= 0.246 Angle : 0.577 10.393 10015 Z= 0.294 Chirality : 0.041 0.128 1182 Planarity : 0.003 0.029 1260 Dihedral : 5.403 59.530 1013 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.85 % Allowed : 13.15 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.27), residues: 928 helix: 0.56 (0.26), residues: 413 sheet: -1.32 (0.35), residues: 183 loop : -1.68 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.023 0.002 PHE R 284 TYR 0.019 0.002 TYR A 230 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.780 Fit side-chains REVERT: R 109 PHE cc_start: 0.8033 (m-80) cc_final: 0.7807 (m-80) REVERT: R 115 LYS cc_start: 0.5275 (mtpp) cc_final: 0.4734 (mmpt) REVERT: R 260 MET cc_start: 0.6134 (mmp) cc_final: 0.5872 (tpp) REVERT: R 289 ASP cc_start: 0.8049 (m-30) cc_final: 0.7825 (m-30) REVERT: R 327 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7695 (m) REVERT: A 22 ASN cc_start: 0.8064 (m110) cc_final: 0.7831 (m110) REVERT: A 198 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7533 (mpt) REVERT: B 111 TYR cc_start: 0.8693 (m-80) cc_final: 0.8471 (m-80) REVERT: B 127 LYS cc_start: 0.7800 (mmtp) cc_final: 0.7162 (mmtp) REVERT: B 259 GLN cc_start: 0.7514 (tp40) cc_final: 0.7178 (tp40) REVERT: P 30 MET cc_start: 0.7932 (ttm) cc_final: 0.7728 (ptp) outliers start: 29 outliers final: 12 residues processed: 138 average time/residue: 0.9494 time to fit residues: 140.7840 Evaluate side-chains 131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 284 PHE Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.169230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128294 restraints weight = 8094.345| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.22 r_work: 0.3369 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7366 Z= 0.273 Angle : 0.600 11.039 10015 Z= 0.302 Chirality : 0.041 0.126 1182 Planarity : 0.003 0.030 1260 Dihedral : 5.506 59.344 1013 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.05 % Allowed : 16.47 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 928 helix: 0.82 (0.26), residues: 413 sheet: -1.32 (0.36), residues: 180 loop : -1.55 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.002 PHE B 253 TYR 0.021 0.002 TYR A 230 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.773 Fit side-chains REVERT: R 115 LYS cc_start: 0.5388 (mtpp) cc_final: 0.4787 (mmpt) REVERT: R 185 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6027 (m90) REVERT: R 260 MET cc_start: 0.6166 (mmp) cc_final: 0.5963 (tpp) REVERT: R 327 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7875 (m) REVERT: A 22 ASN cc_start: 0.8044 (m110) cc_final: 0.7827 (m110) REVERT: A 28 GLU cc_start: 0.7618 (pt0) cc_final: 0.7371 (pt0) REVERT: A 197 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8422 (mtpp) REVERT: A 198 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7774 (mpt) REVERT: B 127 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7414 (mmtp) REVERT: B 258 ASP cc_start: 0.7315 (t0) cc_final: 0.7094 (t0) REVERT: B 259 GLN cc_start: 0.7671 (tp40) cc_final: 0.7323 (tp40) REVERT: B 262 MET cc_start: 0.7697 (ttp) cc_final: 0.7303 (ttp) REVERT: B 336 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8388 (tt) REVERT: P 30 MET cc_start: 0.8027 (ttm) cc_final: 0.7783 (ttm) outliers start: 23 outliers final: 11 residues processed: 134 average time/residue: 0.9927 time to fit residues: 142.2006 Evaluate side-chains 133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.169138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.127924 restraints weight = 8015.189| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.38 r_work: 0.3341 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7366 Z= 0.238 Angle : 0.589 11.300 10015 Z= 0.295 Chirality : 0.041 0.132 1182 Planarity : 0.003 0.030 1260 Dihedral : 5.484 59.114 1013 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.59 % Allowed : 17.53 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.27), residues: 928 helix: 1.03 (0.26), residues: 411 sheet: -1.33 (0.35), residues: 179 loop : -1.53 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.016 0.001 HIS R 185 PHE 0.018 0.002 PHE R 284 TYR 0.022 0.002 TYR A 230 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: R 115 LYS cc_start: 0.5242 (mtpp) cc_final: 0.4656 (mmpt) REVERT: R 260 MET cc_start: 0.6307 (mmp) cc_final: 0.6068 (tpp) REVERT: R 327 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7915 (m) REVERT: A 22 ASN cc_start: 0.8002 (m110) cc_final: 0.7780 (m110) REVERT: A 28 GLU cc_start: 0.7450 (pt0) cc_final: 0.7221 (pt0) REVERT: A 198 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7590 (mpt) REVERT: B 127 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7528 (mmtp) REVERT: B 259 GLN cc_start: 0.7624 (tp40) cc_final: 0.7335 (tp40) REVERT: B 269 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6366 (tt) REVERT: B 336 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8350 (tt) REVERT: P 30 MET cc_start: 0.7959 (ttm) cc_final: 0.7715 (ttm) outliers start: 27 outliers final: 14 residues processed: 130 average time/residue: 0.9374 time to fit residues: 130.7092 Evaluate side-chains 131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.169426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126461 restraints weight = 8090.847| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.41 r_work: 0.3334 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7366 Z= 0.238 Angle : 0.595 11.285 10015 Z= 0.300 Chirality : 0.041 0.127 1182 Planarity : 0.003 0.031 1260 Dihedral : 5.459 58.826 1013 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.59 % Allowed : 18.73 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 928 helix: 1.13 (0.26), residues: 406 sheet: -1.32 (0.35), residues: 178 loop : -1.42 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 107 HIS 0.005 0.001 HIS R 185 PHE 0.014 0.001 PHE B 253 TYR 0.022 0.001 TYR A 230 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.800 Fit side-chains REVERT: R 185 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.6194 (m-70) REVERT: R 260 MET cc_start: 0.6386 (mmp) cc_final: 0.6121 (tpp) REVERT: R 327 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7960 (m) REVERT: A 14 GLU cc_start: 0.7473 (tp30) cc_final: 0.7234 (tp30) REVERT: A 22 ASN cc_start: 0.8036 (m110) cc_final: 0.7806 (m110) REVERT: A 28 GLU cc_start: 0.7522 (pt0) cc_final: 0.7287 (pt0) REVERT: A 198 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7566 (mpt) REVERT: A 308 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: B 259 GLN cc_start: 0.7613 (tp40) cc_final: 0.7348 (tp40) REVERT: B 269 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6259 (tt) REVERT: B 336 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8362 (tt) outliers start: 27 outliers final: 16 residues processed: 133 average time/residue: 0.8989 time to fit residues: 128.5273 Evaluate side-chains 136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 185 HIS R 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.168790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124912 restraints weight = 8039.583| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.51 r_work: 0.3329 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7366 Z= 0.247 Angle : 0.610 11.534 10015 Z= 0.306 Chirality : 0.041 0.144 1182 Planarity : 0.003 0.032 1260 Dihedral : 5.454 58.008 1013 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.59 % Allowed : 19.39 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.27), residues: 928 helix: 1.19 (0.26), residues: 405 sheet: -1.21 (0.36), residues: 174 loop : -1.41 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 107 HIS 0.017 0.001 HIS R 185 PHE 0.013 0.002 PHE R 184 TYR 0.021 0.001 TYR A 230 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: R 260 MET cc_start: 0.6289 (mmp) cc_final: 0.6066 (tpp) REVERT: R 327 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7970 (m) REVERT: A 14 GLU cc_start: 0.7617 (tp30) cc_final: 0.7358 (tp30) REVERT: A 22 ASN cc_start: 0.8023 (m110) cc_final: 0.7782 (m110) REVERT: A 28 GLU cc_start: 0.7463 (pt0) cc_final: 0.7219 (pt0) REVERT: A 198 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7479 (mpt) REVERT: A 308 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: B 259 GLN cc_start: 0.7631 (tp40) cc_final: 0.7389 (tp40) REVERT: B 269 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6298 (tt) REVERT: B 336 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8375 (tt) REVERT: P 30 MET cc_start: 0.7817 (ttm) cc_final: 0.7607 (ptp) outliers start: 27 outliers final: 15 residues processed: 134 average time/residue: 0.9443 time to fit residues: 135.8150 Evaluate side-chains 139 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 78 optimal weight: 0.0370 chunk 77 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126734 restraints weight = 8125.549| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.50 r_work: 0.3348 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7366 Z= 0.209 Angle : 0.602 11.428 10015 Z= 0.302 Chirality : 0.041 0.149 1182 Planarity : 0.003 0.034 1260 Dihedral : 5.403 57.991 1013 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.72 % Allowed : 20.32 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 928 helix: 1.25 (0.27), residues: 404 sheet: -1.17 (0.36), residues: 179 loop : -1.36 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 107 HIS 0.003 0.001 HIS R 188 PHE 0.013 0.001 PHE R 88 TYR 0.019 0.001 TYR A 230 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 327 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7893 (m) REVERT: A 14 GLU cc_start: 0.7640 (tp30) cc_final: 0.7367 (tp30) REVERT: A 22 ASN cc_start: 0.8053 (m110) cc_final: 0.7775 (m110) REVERT: A 28 GLU cc_start: 0.7491 (pt0) cc_final: 0.7253 (pt0) REVERT: A 198 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7513 (mpt) REVERT: A 308 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: B 145 TYR cc_start: 0.8795 (p90) cc_final: 0.8491 (p90) REVERT: B 269 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6207 (tt) REVERT: B 336 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8324 (tt) REVERT: P 30 MET cc_start: 0.7774 (ttm) cc_final: 0.7566 (ptp) outliers start: 28 outliers final: 15 residues processed: 140 average time/residue: 0.9544 time to fit residues: 143.2944 Evaluate side-chains 135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 54 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 70 optimal weight: 0.0010 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 84 optimal weight: 0.0000 chunk 51 optimal weight: 8.9990 chunk 88 optimal weight: 0.0020 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 222 GLN R 264 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.173531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129995 restraints weight = 8156.422| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.45 r_work: 0.3400 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7366 Z= 0.177 Angle : 0.616 11.378 10015 Z= 0.309 Chirality : 0.040 0.153 1182 Planarity : 0.003 0.034 1260 Dihedral : 5.307 57.735 1013 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.19 % Allowed : 21.78 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 928 helix: 1.34 (0.27), residues: 403 sheet: -1.11 (0.37), residues: 167 loop : -1.32 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 107 HIS 0.003 0.001 HIS R 188 PHE 0.014 0.001 PHE R 88 TYR 0.017 0.001 TYR A 230 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7824 (m) REVERT: A 14 GLU cc_start: 0.7661 (tp30) cc_final: 0.7387 (tp30) REVERT: A 22 ASN cc_start: 0.7984 (m110) cc_final: 0.7747 (m110) REVERT: A 198 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7458 (mpt) REVERT: A 207 GLU cc_start: 0.8433 (tt0) cc_final: 0.8079 (tp30) REVERT: A 308 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: B 269 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6096 (tt) REVERT: B 336 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8279 (tt) outliers start: 24 outliers final: 12 residues processed: 133 average time/residue: 0.9248 time to fit residues: 132.2551 Evaluate side-chains 132 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 0.0370 chunk 86 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 264 ASN B 239 ASN ** B 259 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 = 0.4008 r_free = 0.4008 target = 0.167105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125039 restraints weight = 8306.097| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.39 r_work: 0.3306 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7366 Z= 0.298 Angle : 0.680 11.152 10015 Z= 0.340 Chirality : 0.043 0.167 1182 Planarity : 0.003 0.035 1260 Dihedral : 5.479 56.751 1013 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.66 % Allowed : 22.71 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 928 helix: 1.26 (0.26), residues: 403 sheet: -1.07 (0.38), residues: 174 loop : -1.32 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 258 HIS 0.006 0.001 HIS B 142 PHE 0.013 0.002 PHE R 88 TYR 0.018 0.002 TYR A 230 ARG 0.006 0.000 ARG R 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 327 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8080 (m) REVERT: A 14 GLU cc_start: 0.7730 (tp30) cc_final: 0.7513 (tp30) REVERT: A 198 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7493 (mpt) REVERT: A 207 GLU cc_start: 0.8498 (tt0) cc_final: 0.8093 (tp30) REVERT: A 308 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 269 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6331 (tt) REVERT: B 336 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8461 (tt) outliers start: 20 outliers final: 11 residues processed: 129 average time/residue: 1.0019 time to fit residues: 138.0052 Evaluate side-chains 127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain P residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 145 ASN R 222 GLN A 22 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123001 restraints weight = 8107.813| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.47 r_work: 0.3362 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7366 Z= 0.235 Angle : 0.665 11.655 10015 Z= 0.330 Chirality : 0.041 0.163 1182 Planarity : 0.003 0.035 1260 Dihedral : 5.489 57.449 1013 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.39 % Allowed : 22.97 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.28), residues: 928 helix: 1.21 (0.26), residues: 403 sheet: -1.05 (0.38), residues: 174 loop : -1.26 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 107 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE R 88 TYR 0.016 0.002 TYR A 230 ARG 0.003 0.000 ARG P 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.77 seconds wall clock time: 89 minutes 31.54 seconds (5371.54 seconds total)