Starting phenix.real_space_refine on Fri Aug 22 23:07:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9w_27966/08_2025/8e9w_27966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9w_27966/08_2025/8e9w_27966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e9w_27966/08_2025/8e9w_27966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9w_27966/08_2025/8e9w_27966.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9w_27966/08_2025/8e9w_27966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9w_27966/08_2025/8e9w_27966.cif" } resolution = 2.69 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5451 2.51 5 N 1450 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8529 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2187 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1669 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2505 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 405 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1741 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'WEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.52, per 1000 atoms: 0.18 Number of scatterers: 8529 At special positions: 0 Unit cell: (116.16, 104.72, 124.08, 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 56 16.00 O 1572 8.00 N 1450 7.00 C 5451 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 0.57 Conformation dependent library (CDL) restraints added in 353.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 37.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 64 through 96 removed outlier: 5.436A pdb=" N PHE A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.656A pdb=" N ILE A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 172 removed outlier: 4.046A pdb=" N TRP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.524A pdb=" N MET A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 230 through 240 Processing helix chain 'A' and resid 240 through 265 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.858A pdb=" N GLN A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 517 Proline residue: A 506 - end of helix removed outlier: 3.956A pdb=" N LEU A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.978A pdb=" N TYR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER A 537 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.532A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 4.329A pdb=" N GLY B 45 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 4.106A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.235A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.645A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 184 through 204 removed outlier: 3.596A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 Processing helix chain 'C' and resid 3 through 24 removed outlier: 3.515A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 4.107A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 6.427A pdb=" N LEU B 34 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE B 84 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 36 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL B 86 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU B 38 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.791A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.615A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.853A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.387A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.623A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.697A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.746A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.045A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.516A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1197 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: 1.13 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1621 1.33 - 1.45: 2253 1.45 - 1.57: 4760 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 8713 Sorted by residual: bond pdb=" C01 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.455 1.286 0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C06 WEC A 601 " pdb=" N07 WEC A 601 " ideal model delta sigma weight residual 1.292 1.452 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C06 WEC A 601 " pdb=" N05 WEC A 601 " ideal model delta sigma weight residual 1.373 1.499 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C03 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.461 1.371 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C22 WEC A 601 " pdb=" N02 WEC A 601 " ideal model delta sigma weight residual 1.459 1.372 0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 8708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11632 1.92 - 3.84: 185 3.84 - 5.77: 35 5.77 - 7.69: 8 7.69 - 9.61: 5 Bond angle restraints: 11865 Sorted by residual: angle pdb=" N PHE B 167 " pdb=" CA PHE B 167 " pdb=" C PHE B 167 " ideal model delta sigma weight residual 113.18 103.57 9.61 1.21e+00 6.83e-01 6.31e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " ideal model delta sigma weight residual 118.03 125.61 -7.58 1.19e+00 7.06e-01 4.06e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" O TYR E 223 " ideal model delta sigma weight residual 120.23 113.82 6.41 1.02e+00 9.61e-01 3.95e+01 angle pdb=" N PRO B 184 " pdb=" CA PRO B 184 " pdb=" C PRO B 184 " ideal model delta sigma weight residual 113.53 105.08 8.45 1.39e+00 5.18e-01 3.70e+01 angle pdb=" O PHE B 164 " pdb=" C PHE B 164 " pdb=" N PRO B 165 " ideal model delta sigma weight residual 120.83 114.42 6.41 1.06e+00 8.90e-01 3.66e+01 ... (remaining 11860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4671 17.34 - 34.67: 358 34.67 - 52.01: 60 52.01 - 69.34: 11 69.34 - 86.68: 4 Dihedral angle restraints: 5104 sinusoidal: 1844 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual -86.00 -168.18 82.18 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 147.71 -54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " pdb=" SG CYS A 221 " pdb=" CB CYS A 221 " ideal model delta sinusoidal sigma weight residual -86.00 -137.28 51.28 1 1.00e+01 1.00e-02 3.60e+01 ... (remaining 5101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1176 0.059 - 0.118: 190 0.118 - 0.177: 9 0.177 - 0.236: 2 0.236 - 0.295: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA THR B 171 " pdb=" N THR B 171 " pdb=" C THR B 171 " pdb=" CB THR B 171 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA TYR E 223 " pdb=" N TYR E 223 " pdb=" C TYR E 223 " pdb=" CB TYR E 223 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ARG B 169 " pdb=" N ARG B 169 " pdb=" C ARG B 169 " pdb=" CB ARG B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1375 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 171 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C THR B 171 " -0.062 2.00e-02 2.50e+03 pdb=" O THR B 171 " 0.023 2.00e-02 2.50e+03 pdb=" N THR B 172 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 183 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C LYS A 183 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 183 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 184 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 54 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO D 55 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 879 2.75 - 3.29: 8307 3.29 - 3.82: 14124 3.82 - 4.36: 16892 4.36 - 4.90: 29622 Nonbonded interactions: 69824 Sorted by model distance: nonbonded pdb=" O LEU A 512 " pdb=" OG1 THR A 515 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.214 3.040 nonbonded pdb=" O LEU A 88 " pdb=" OG SER A 92 " model vdw 2.230 3.040 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.234 3.040 nonbonded pdb=" NH1 ARG C 49 " pdb=" O TYR C 85 " model vdw 2.243 3.120 ... (remaining 69819 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 0.169 8716 Z= 0.255 Angle : 0.628 9.611 11871 Z= 0.374 Chirality : 0.043 0.295 1378 Planarity : 0.003 0.041 1497 Dihedral : 12.691 86.677 2989 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.11 % Allowed : 0.23 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.23 (0.26), residues: 1103 helix: 0.42 (0.27), residues: 377 sheet: 0.92 (0.32), residues: 285 loop : -0.49 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.016 0.001 TYR E 178 PHE 0.012 0.001 PHE C 234 TRP 0.009 0.001 TRP C 82 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8713) covalent geometry : angle 0.62811 (11865) SS BOND : bond 0.00300 ( 3) SS BOND : angle 0.78490 ( 6) hydrogen bonds : bond 0.23087 ( 423) hydrogen bonds : angle 7.68184 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7368 (m-30) cc_final: 0.7094 (m-30) REVERT: B 99 CYS cc_start: 0.7800 (m) cc_final: 0.7497 (m) REVERT: C 98 SER cc_start: 0.8314 (p) cc_final: 0.8111 (t) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.3690 time to fit residues: 67.0145 Evaluate side-chains 156 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN C 125 ASN C 266 HIS C 340 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114043 restraints weight = 11920.257| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.79 r_work: 0.3379 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8716 Z= 0.182 Angle : 0.580 8.040 11871 Z= 0.306 Chirality : 0.044 0.141 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.676 35.390 1224 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.25 % Allowed : 9.24 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.66 (0.26), residues: 1103 helix: 1.08 (0.27), residues: 401 sheet: 0.67 (0.31), residues: 298 loop : -0.26 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 219 TYR 0.023 0.002 TYR E 178 PHE 0.012 0.002 PHE B 74 TRP 0.018 0.002 TRP C 169 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8713) covalent geometry : angle 0.57965 (11865) SS BOND : bond 0.00549 ( 3) SS BOND : angle 0.74995 ( 6) hydrogen bonds : bond 0.05576 ( 423) hydrogen bonds : angle 5.15492 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.239 Fit side-chains REVERT: A 88 LEU cc_start: 0.7779 (mp) cc_final: 0.7520 (mp) REVERT: B 20 ASP cc_start: 0.7906 (m-30) cc_final: 0.7533 (m-30) REVERT: B 128 ILE cc_start: 0.8406 (tp) cc_final: 0.8094 (tp) REVERT: C 98 SER cc_start: 0.8561 (p) cc_final: 0.8262 (t) REVERT: C 160 SER cc_start: 0.8286 (t) cc_final: 0.7928 (p) REVERT: E 19 LYS cc_start: 0.8472 (tttp) cc_final: 0.8263 (tttm) REVERT: E 86 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8073 (pp) REVERT: E 190 ARG cc_start: 0.8287 (ptt-90) cc_final: 0.7920 (ptt180) outliers start: 11 outliers final: 4 residues processed: 181 average time/residue: 0.4081 time to fit residues: 78.8221 Evaluate side-chains 175 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN C 119 ASN C 125 ASN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114580 restraints weight = 11701.961| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.79 r_work: 0.3389 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8716 Z= 0.162 Angle : 0.547 9.328 11871 Z= 0.286 Chirality : 0.043 0.136 1378 Planarity : 0.004 0.040 1497 Dihedral : 4.657 35.717 1224 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.60 % Allowed : 13.11 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 1103 helix: 1.22 (0.28), residues: 402 sheet: 0.49 (0.31), residues: 295 loop : -0.22 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.022 0.001 TYR E 178 PHE 0.013 0.001 PHE B 74 TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8713) covalent geometry : angle 0.54717 (11865) SS BOND : bond 0.00499 ( 3) SS BOND : angle 0.66361 ( 6) hydrogen bonds : bond 0.04749 ( 423) hydrogen bonds : angle 4.75203 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.308 Fit side-chains REVERT: A 88 LEU cc_start: 0.7833 (mp) cc_final: 0.7597 (mp) REVERT: B 20 ASP cc_start: 0.7855 (m-30) cc_final: 0.7512 (m-30) REVERT: B 99 CYS cc_start: 0.8465 (m) cc_final: 0.8220 (m) REVERT: B 200 ILE cc_start: 0.7722 (mt) cc_final: 0.7465 (mp) REVERT: C 98 SER cc_start: 0.8574 (p) cc_final: 0.8169 (t) REVERT: E 190 ARG cc_start: 0.8303 (ptt-90) cc_final: 0.7881 (ptt180) outliers start: 14 outliers final: 6 residues processed: 166 average time/residue: 0.3671 time to fit residues: 65.7620 Evaluate side-chains 162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 125 ASN C 295 ASN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.133309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114603 restraints weight = 11961.499| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.82 r_work: 0.3395 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8716 Z= 0.139 Angle : 0.522 8.843 11871 Z= 0.275 Chirality : 0.042 0.133 1378 Planarity : 0.004 0.040 1497 Dihedral : 4.556 35.046 1224 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.05 % Allowed : 14.71 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.76 (0.26), residues: 1103 helix: 1.35 (0.28), residues: 402 sheet: 0.47 (0.31), residues: 299 loop : -0.22 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.021 0.001 TYR E 178 PHE 0.013 0.001 PHE B 74 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8713) covalent geometry : angle 0.52201 (11865) SS BOND : bond 0.00408 ( 3) SS BOND : angle 0.61672 ( 6) hydrogen bonds : bond 0.04273 ( 423) hydrogen bonds : angle 4.58692 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.243 Fit side-chains REVERT: A 88 LEU cc_start: 0.7870 (mp) cc_final: 0.7628 (mp) REVERT: B 20 ASP cc_start: 0.7873 (m-30) cc_final: 0.7574 (m-30) REVERT: B 99 CYS cc_start: 0.8455 (m) cc_final: 0.8197 (m) REVERT: B 200 ILE cc_start: 0.7739 (mt) cc_final: 0.7474 (mp) REVERT: C 98 SER cc_start: 0.8571 (p) cc_final: 0.8146 (t) REVERT: E 190 ARG cc_start: 0.8267 (ptt-90) cc_final: 0.8008 (ptt180) outliers start: 18 outliers final: 11 residues processed: 166 average time/residue: 0.3575 time to fit residues: 63.9597 Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113680 restraints weight = 11914.822| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.82 r_work: 0.3379 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8716 Z= 0.173 Angle : 0.549 10.698 11871 Z= 0.287 Chirality : 0.043 0.161 1378 Planarity : 0.004 0.040 1497 Dihedral : 4.655 35.861 1224 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.62 % Allowed : 15.85 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.71 (0.26), residues: 1103 helix: 1.33 (0.28), residues: 403 sheet: 0.42 (0.30), residues: 301 loop : -0.24 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.022 0.001 TYR E 178 PHE 0.014 0.001 PHE B 74 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8713) covalent geometry : angle 0.54876 (11865) SS BOND : bond 0.00513 ( 3) SS BOND : angle 0.80012 ( 6) hydrogen bonds : bond 0.04444 ( 423) hydrogen bonds : angle 4.61411 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.206 Fit side-chains REVERT: B 20 ASP cc_start: 0.7854 (m-30) cc_final: 0.7503 (m-30) REVERT: B 99 CYS cc_start: 0.8459 (m) cc_final: 0.8213 (m) REVERT: C 98 SER cc_start: 0.8571 (p) cc_final: 0.8136 (t) REVERT: C 293 ASN cc_start: 0.8257 (p0) cc_final: 0.8049 (p0) REVERT: E 190 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.7850 (ptt180) outliers start: 23 outliers final: 14 residues processed: 183 average time/residue: 0.3775 time to fit residues: 73.9064 Evaluate side-chains 182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 229 ASN B 244 ASN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114158 restraints weight = 11766.519| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.80 r_work: 0.3387 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8716 Z= 0.166 Angle : 0.552 10.679 11871 Z= 0.287 Chirality : 0.043 0.190 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.646 34.695 1224 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.96 % Allowed : 16.08 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.74 (0.26), residues: 1103 helix: 1.36 (0.28), residues: 403 sheet: 0.38 (0.30), residues: 303 loop : -0.20 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.022 0.001 TYR E 178 PHE 0.013 0.001 PHE B 74 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8713) covalent geometry : angle 0.55136 (11865) SS BOND : bond 0.00474 ( 3) SS BOND : angle 0.79531 ( 6) hydrogen bonds : bond 0.04318 ( 423) hydrogen bonds : angle 4.58029 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7851 (m-30) cc_final: 0.7490 (m-30) REVERT: B 99 CYS cc_start: 0.8439 (m) cc_final: 0.8194 (m) REVERT: B 147 ASP cc_start: 0.8144 (p0) cc_final: 0.7323 (p0) REVERT: B 151 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: C 98 SER cc_start: 0.8568 (p) cc_final: 0.8135 (t) REVERT: E 87 ARG cc_start: 0.8105 (ptp90) cc_final: 0.7822 (ptt90) REVERT: E 190 ARG cc_start: 0.8280 (ptt-90) cc_final: 0.7868 (ptt180) outliers start: 26 outliers final: 16 residues processed: 182 average time/residue: 0.4147 time to fit residues: 80.4491 Evaluate side-chains 185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 0.0270 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 70 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 86 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.1628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 123 ASN B 144 ASN B 244 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117181 restraints weight = 11900.363| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.81 r_work: 0.3434 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8716 Z= 0.096 Angle : 0.495 7.767 11871 Z= 0.260 Chirality : 0.041 0.138 1378 Planarity : 0.003 0.041 1497 Dihedral : 4.289 30.888 1224 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.51 % Allowed : 16.53 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.95 (0.26), residues: 1103 helix: 1.67 (0.28), residues: 398 sheet: 0.52 (0.31), residues: 277 loop : -0.19 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.024 0.001 TYR E 178 PHE 0.011 0.001 PHE B 74 TRP 0.017 0.001 TRP C 169 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 8713) covalent geometry : angle 0.49517 (11865) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.40113 ( 6) hydrogen bonds : bond 0.03481 ( 423) hydrogen bonds : angle 4.29841 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7860 (m-30) cc_final: 0.7527 (m-30) REVERT: B 24 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7251 (ptp90) REVERT: B 147 ASP cc_start: 0.8153 (p0) cc_final: 0.7303 (p0) REVERT: B 151 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5883 (mp0) REVERT: B 200 ILE cc_start: 0.7649 (mt) cc_final: 0.7398 (mp) REVERT: C 98 SER cc_start: 0.8539 (p) cc_final: 0.8121 (t) REVERT: C 258 ASP cc_start: 0.7642 (t0) cc_final: 0.7325 (t0) REVERT: E 137 VAL cc_start: 0.8230 (t) cc_final: 0.7910 (p) REVERT: E 211 ASP cc_start: 0.7921 (t0) cc_final: 0.7674 (m-30) outliers start: 22 outliers final: 12 residues processed: 171 average time/residue: 0.3431 time to fit residues: 63.4986 Evaluate side-chains 170 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN B 144 ASN B 229 ASN B 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.133084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114577 restraints weight = 11782.072| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.81 r_work: 0.3397 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8716 Z= 0.151 Angle : 0.543 8.606 11871 Z= 0.283 Chirality : 0.043 0.176 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.481 33.819 1224 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.51 % Allowed : 17.56 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.93 (0.26), residues: 1103 helix: 1.60 (0.28), residues: 402 sheet: 0.46 (0.30), residues: 296 loop : -0.13 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.019 0.001 TYR E 178 PHE 0.013 0.001 PHE A 225 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8713) covalent geometry : angle 0.54240 (11865) SS BOND : bond 0.00383 ( 3) SS BOND : angle 0.73917 ( 6) hydrogen bonds : bond 0.04014 ( 423) hydrogen bonds : angle 4.39011 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8085 (p90) cc_final: 0.7869 (p90) REVERT: B 20 ASP cc_start: 0.7855 (m-30) cc_final: 0.7528 (m-30) REVERT: B 24 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7194 (ptp90) REVERT: B 99 CYS cc_start: 0.8437 (m) cc_final: 0.8196 (m) REVERT: B 147 ASP cc_start: 0.8115 (p0) cc_final: 0.7281 (p0) REVERT: B 151 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5939 (mp0) REVERT: C 98 SER cc_start: 0.8569 (p) cc_final: 0.8133 (t) REVERT: E 190 ARG cc_start: 0.8261 (ptt-90) cc_final: 0.8024 (ptt180) REVERT: E 211 ASP cc_start: 0.7933 (t0) cc_final: 0.7347 (m-30) outliers start: 22 outliers final: 13 residues processed: 178 average time/residue: 0.3864 time to fit residues: 73.8077 Evaluate side-chains 179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 244 ASN C 125 ASN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115317 restraints weight = 11725.995| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.80 r_work: 0.3410 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8716 Z= 0.125 Angle : 0.530 8.522 11871 Z= 0.277 Chirality : 0.042 0.154 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.435 32.900 1224 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.74 % Allowed : 17.79 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.96 (0.26), residues: 1103 helix: 1.63 (0.28), residues: 401 sheet: 0.43 (0.30), residues: 297 loop : -0.09 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.021 0.001 TYR E 178 PHE 0.012 0.001 PHE B 74 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8713) covalent geometry : angle 0.53010 (11865) SS BOND : bond 0.00320 ( 3) SS BOND : angle 0.65093 ( 6) hydrogen bonds : bond 0.03803 ( 423) hydrogen bonds : angle 4.34592 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 225 PHE cc_start: 0.8037 (p90) cc_final: 0.7822 (p90) REVERT: B 20 ASP cc_start: 0.7847 (m-30) cc_final: 0.7519 (m-30) REVERT: B 99 CYS cc_start: 0.8399 (m) cc_final: 0.8152 (m) REVERT: B 147 ASP cc_start: 0.8108 (p0) cc_final: 0.7284 (p0) REVERT: B 151 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5939 (mp0) REVERT: C 98 SER cc_start: 0.8559 (p) cc_final: 0.8134 (t) REVERT: C 258 ASP cc_start: 0.7675 (t0) cc_final: 0.7367 (t0) REVERT: E 137 VAL cc_start: 0.8260 (t) cc_final: 0.7952 (p) outliers start: 24 outliers final: 15 residues processed: 183 average time/residue: 0.3951 time to fit residues: 77.4155 Evaluate side-chains 186 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 244 ASN C 125 ASN C 230 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114256 restraints weight = 11770.978| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.80 r_work: 0.3388 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8716 Z= 0.161 Angle : 0.564 9.728 11871 Z= 0.293 Chirality : 0.043 0.180 1378 Planarity : 0.004 0.049 1497 Dihedral : 4.611 34.273 1224 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.17 % Allowed : 18.59 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.92 (0.26), residues: 1103 helix: 1.56 (0.28), residues: 401 sheet: 0.47 (0.30), residues: 300 loop : -0.14 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 24 TYR 0.019 0.001 TYR E 178 PHE 0.013 0.001 PHE A 225 TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8713) covalent geometry : angle 0.56376 (11865) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.82886 ( 6) hydrogen bonds : bond 0.04091 ( 423) hydrogen bonds : angle 4.41680 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7871 (m-30) cc_final: 0.7575 (m-30) REVERT: B 99 CYS cc_start: 0.8409 (m) cc_final: 0.8159 (m) REVERT: B 147 ASP cc_start: 0.8101 (p0) cc_final: 0.7337 (p0) REVERT: B 151 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: C 98 SER cc_start: 0.8572 (p) cc_final: 0.8141 (t) REVERT: C 258 ASP cc_start: 0.7690 (t0) cc_final: 0.7386 (t0) REVERT: E 190 ARG cc_start: 0.8142 (ptt180) cc_final: 0.7793 (ptt180) REVERT: E 211 ASP cc_start: 0.7805 (t0) cc_final: 0.7299 (m-30) outliers start: 19 outliers final: 16 residues processed: 177 average time/residue: 0.4212 time to fit residues: 79.6056 Evaluate side-chains 184 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 244 ASN C 125 ASN E 167 GLN E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112110 restraints weight = 11753.656| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.81 r_work: 0.3370 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8716 Z= 0.214 Angle : 0.619 12.895 11871 Z= 0.319 Chirality : 0.045 0.193 1378 Planarity : 0.004 0.061 1497 Dihedral : 4.841 36.734 1224 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.28 % Allowed : 18.81 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.78 (0.26), residues: 1103 helix: 1.39 (0.27), residues: 402 sheet: 0.44 (0.30), residues: 301 loop : -0.19 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 24 TYR 0.018 0.002 TYR E 178 PHE 0.025 0.002 PHE A 225 TRP 0.015 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 8713) covalent geometry : angle 0.61864 (11865) SS BOND : bond 0.00544 ( 3) SS BOND : angle 1.03025 ( 6) hydrogen bonds : bond 0.04579 ( 423) hydrogen bonds : angle 4.59955 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2752.67 seconds wall clock time: 47 minutes 31.37 seconds (2851.37 seconds total)