Starting phenix.real_space_refine on Sat Dec 28 12:27:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e9w_27966/12_2024/8e9w_27966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9w_27966/12_2024/8e9w_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_27966/12_2024/8e9w_27966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9w_27966/12_2024/8e9w_27966.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9w_27966/12_2024/8e9w_27966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9w_27966/12_2024/8e9w_27966.cif" } resolution = 2.69 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'ARG:plan': 1, 'TRP: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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP: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: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP: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, 'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 1, 'GLU:plan': 7, '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: 5.83, per 1000 atoms: 0.68 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.93 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: 2.57 Time building geometry restraints manager: 2.65 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: 1.730 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- 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 8713 Z= 0.341 Angle : 0.628 9.611 11865 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 : 7.31 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 (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: 0.23 (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 TRP 0.009 0.001 TRP C 82 HIS 0.002 0.001 HIS B 82 PHE 0.012 0.001 PHE C 234 TYR 0.016 0.001 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** 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 : 0.996 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: 1.0249 time to fit residues: 186.1158 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 : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8713 Z= 0.276 Angle : 0.581 7.951 11865 Z= 0.307 Chirality : 0.044 0.140 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.690 35.635 1224 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.25 % Allowed : 9.35 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.67 (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 TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS B 209 PHE 0.012 0.002 PHE B 74 TYR 0.023 0.001 TYR E 178 ARG 0.004 0.000 ARG C 219 *********************** 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 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.931 Fit side-chains REVERT: A 88 LEU cc_start: 0.7624 (mp) cc_final: 0.7357 (mp) REVERT: B 20 ASP cc_start: 0.7338 (m-30) cc_final: 0.6967 (m-30) REVERT: B 128 ILE cc_start: 0.8194 (tp) cc_final: 0.7890 (tp) REVERT: C 98 SER cc_start: 0.8346 (p) cc_final: 0.8110 (t) REVERT: C 160 SER cc_start: 0.8031 (t) cc_final: 0.7707 (p) REVERT: E 86 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8072 (pp) REVERT: E 190 ARG cc_start: 0.8217 (ptt-90) cc_final: 0.7865 (ptt180) outliers start: 11 outliers final: 4 residues processed: 178 average time/residue: 1.1790 time to fit residues: 223.7539 Evaluate side-chains 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN C 125 ASN C 340 ASN E 167 GLN E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8713 Z= 0.360 Angle : 0.603 12.236 11865 Z= 0.315 Chirality : 0.045 0.136 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.891 38.754 1224 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.82 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1103 helix: 0.96 (0.27), residues: 403 sheet: 0.48 (0.30), residues: 303 loop : -0.33 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.005 0.001 HIS B 209 PHE 0.015 0.002 PHE B 74 TYR 0.021 0.002 TYR E 178 ARG 0.005 0.000 ARG B 24 *********************** 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 185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.029 Fit side-chains REVERT: A 88 LEU cc_start: 0.7726 (mp) cc_final: 0.7446 (mp) REVERT: B 20 ASP cc_start: 0.7313 (m-30) cc_final: 0.6969 (m-30) REVERT: B 99 CYS cc_start: 0.7789 (m) cc_final: 0.7502 (m) REVERT: C 98 SER cc_start: 0.8377 (p) cc_final: 0.8040 (t) REVERT: E 67 ARG cc_start: 0.8391 (ptt90) cc_final: 0.8185 (ptm-80) REVERT: E 190 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7831 (ptt180) outliers start: 16 outliers final: 9 residues processed: 176 average time/residue: 1.1523 time to fit residues: 216.6249 Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 542 VAL 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 307 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 82 GLN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8713 Z= 0.183 Angle : 0.520 8.927 11865 Z= 0.272 Chirality : 0.042 0.134 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.540 34.005 1224 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.60 % Allowed : 15.51 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.74 (0.26), residues: 1103 helix: 1.33 (0.28), residues: 402 sheet: 0.46 (0.31), residues: 294 loop : -0.22 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.001 HIS B 209 PHE 0.011 0.001 PHE B 74 TYR 0.023 0.001 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** 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 185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.002 Fit side-chains REVERT: A 88 LEU cc_start: 0.7694 (mp) cc_final: 0.7448 (mp) REVERT: B 20 ASP cc_start: 0.7286 (m-30) cc_final: 0.6965 (m-30) REVERT: B 99 CYS cc_start: 0.7743 (m) cc_final: 0.7434 (m) REVERT: B 200 ILE cc_start: 0.7600 (mt) cc_final: 0.7352 (mp) REVERT: C 98 SER cc_start: 0.8364 (p) cc_final: 0.7992 (t) REVERT: C 290 ASP cc_start: 0.7298 (m-30) cc_final: 0.7078 (m-30) REVERT: E 190 ARG cc_start: 0.8204 (ptt-90) cc_final: 0.7821 (ptt180) outliers start: 14 outliers final: 6 residues processed: 177 average time/residue: 1.1034 time to fit residues: 209.3370 Evaluate side-chains 170 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 128 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 110 ASN C 125 ASN C 295 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8713 Z= 0.267 Angle : 0.556 11.060 11865 Z= 0.289 Chirality : 0.044 0.182 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.679 35.766 1224 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.85 % Allowed : 15.62 % 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 (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: 0.67 (0.26), residues: 1103 helix: 1.28 (0.27), residues: 403 sheet: 0.44 (0.30), residues: 299 loop : -0.27 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS B 209 PHE 0.023 0.001 PHE A 225 TYR 0.022 0.001 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** 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 191 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.013 Fit side-chains REVERT: B 20 ASP cc_start: 0.7305 (m-30) cc_final: 0.6976 (m-30) REVERT: B 99 CYS cc_start: 0.7771 (m) cc_final: 0.7472 (m) REVERT: C 98 SER cc_start: 0.8379 (p) cc_final: 0.7981 (t) REVERT: E 190 ARG cc_start: 0.8214 (ptt-90) cc_final: 0.7968 (ptt180) outliers start: 25 outliers final: 13 residues processed: 176 average time/residue: 1.1446 time to fit residues: 215.0041 Evaluate side-chains 176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 244 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8713 Z= 0.214 Angle : 0.535 9.784 11865 Z= 0.279 Chirality : 0.043 0.179 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.579 34.235 1224 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.85 % Allowed : 16.08 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.26), residues: 1103 helix: 1.39 (0.27), residues: 403 sheet: 0.40 (0.31), residues: 286 loop : -0.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.020 0.001 PHE A 225 TYR 0.022 0.001 TYR E 178 ARG 0.005 0.000 ARG C 219 *********************** 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 192 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7309 (m-30) cc_final: 0.7058 (m-30) REVERT: B 99 CYS cc_start: 0.7743 (m) cc_final: 0.7443 (m) REVERT: B 147 ASP cc_start: 0.8001 (p0) cc_final: 0.7100 (p0) REVERT: B 151 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5448 (mp0) REVERT: C 98 SER cc_start: 0.8372 (p) cc_final: 0.7979 (t) REVERT: E 87 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7700 (ptt90) REVERT: E 190 ARG cc_start: 0.8209 (ptt-90) cc_final: 0.7817 (ptt180) outliers start: 25 outliers final: 17 residues processed: 176 average time/residue: 1.2010 time to fit residues: 225.6539 Evaluate side-chains 184 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET 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 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 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 11 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 340 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8713 Z= 0.213 Angle : 0.537 9.870 11865 Z= 0.279 Chirality : 0.043 0.181 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.555 33.935 1224 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.39 % Allowed : 17.10 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.79 (0.26), residues: 1103 helix: 1.45 (0.28), residues: 403 sheet: 0.38 (0.30), residues: 297 loop : -0.19 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.018 0.001 PHE A 225 TYR 0.021 0.001 TYR E 178 ARG 0.008 0.000 ARG C 219 *********************** 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 187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7316 (m-30) cc_final: 0.7058 (m-30) REVERT: B 99 CYS cc_start: 0.7742 (m) cc_final: 0.7442 (m) REVERT: B 147 ASP cc_start: 0.8022 (p0) cc_final: 0.7116 (p0) REVERT: B 151 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5456 (mp0) REVERT: C 98 SER cc_start: 0.8372 (p) cc_final: 0.7987 (t) outliers start: 21 outliers final: 16 residues processed: 175 average time/residue: 1.1711 time to fit residues: 218.8453 Evaluate side-chains 177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 110 ASN C 125 ASN C 295 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8713 Z= 0.278 Angle : 0.575 11.970 11865 Z= 0.297 Chirality : 0.044 0.204 1378 Planarity : 0.004 0.041 1497 Dihedral : 4.697 35.340 1224 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.74 % Allowed : 17.45 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.73 (0.26), residues: 1103 helix: 1.36 (0.27), residues: 403 sheet: 0.38 (0.30), residues: 302 loop : -0.21 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.001 PHE A 225 TYR 0.020 0.001 TYR E 178 ARG 0.009 0.000 ARG B 24 *********************** 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 188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7323 (m-30) cc_final: 0.6966 (m-30) REVERT: B 99 CYS cc_start: 0.7750 (m) cc_final: 0.7450 (m) REVERT: B 147 ASP cc_start: 0.7972 (p0) cc_final: 0.7091 (p0) REVERT: B 151 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5584 (mp0) REVERT: C 98 SER cc_start: 0.8373 (p) cc_final: 0.7994 (t) REVERT: E 190 ARG cc_start: 0.8082 (ptt180) cc_final: 0.7812 (ptt180) outliers start: 24 outliers final: 14 residues processed: 172 average time/residue: 1.1821 time to fit residues: 217.0588 Evaluate side-chains 175 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 295 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8713 Z= 0.234 Angle : 0.557 11.133 11865 Z= 0.288 Chirality : 0.043 0.185 1378 Planarity : 0.004 0.049 1497 Dihedral : 4.650 34.283 1224 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.74 % Allowed : 17.90 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.79 (0.26), residues: 1103 helix: 1.42 (0.28), residues: 403 sheet: 0.36 (0.30), residues: 303 loop : -0.14 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE A 225 TYR 0.021 0.001 TYR E 178 ARG 0.013 0.000 ARG B 24 *********************** 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 182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7329 (m-30) cc_final: 0.6995 (m-30) REVERT: B 99 CYS cc_start: 0.7733 (m) cc_final: 0.7422 (m) REVERT: B 147 ASP cc_start: 0.7958 (p0) cc_final: 0.7128 (p0) REVERT: B 151 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5578 (mp0) REVERT: C 98 SER cc_start: 0.8370 (p) cc_final: 0.7991 (t) REVERT: E 190 ARG cc_start: 0.8036 (ptt180) cc_final: 0.7718 (ptt180) REVERT: E 211 ASP cc_start: 0.7427 (t0) cc_final: 0.6945 (m-30) outliers start: 24 outliers final: 15 residues processed: 171 average time/residue: 1.1605 time to fit residues: 213.1569 Evaluate side-chains 172 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.0020 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 125 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8713 Z= 0.189 Angle : 0.537 9.475 11865 Z= 0.279 Chirality : 0.042 0.157 1378 Planarity : 0.004 0.047 1497 Dihedral : 4.508 32.947 1224 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.74 % Allowed : 18.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1103 helix: 1.52 (0.28), residues: 402 sheet: 0.38 (0.31), residues: 292 loop : -0.10 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE A 225 TYR 0.021 0.001 TYR E 178 ARG 0.011 0.000 ARG B 24 ********************** 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: 24 poor density : 164 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7340 (m-30) cc_final: 0.7065 (m-30) REVERT: B 99 CYS cc_start: 0.7728 (m) cc_final: 0.7412 (m) REVERT: B 147 ASP cc_start: 0.7996 (p0) cc_final: 0.7120 (p0) REVERT: B 151 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5549 (mp0) REVERT: B 200 ILE cc_start: 0.7558 (mt) cc_final: 0.7327 (mp) REVERT: C 98 SER cc_start: 0.8361 (p) cc_final: 0.7996 (t) REVERT: E 190 ARG cc_start: 0.8007 (ptt180) cc_final: 0.7720 (ptt180) REVERT: E 211 ASP cc_start: 0.7435 (t0) cc_final: 0.6935 (m-30) outliers start: 24 outliers final: 18 residues processed: 176 average time/residue: 1.1106 time to fit residues: 209.3414 Evaluate side-chains 179 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 256 LYS 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 125 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.0020 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 110 ASN C 125 ASN C 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115101 restraints weight = 11652.573| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.79 r_work: 0.3404 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8713 Z= 0.205 Angle : 0.541 9.595 11865 Z= 0.282 Chirality : 0.043 0.190 1378 Planarity : 0.004 0.044 1497 Dihedral : 4.535 33.120 1224 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.51 % Allowed : 19.16 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.89 (0.26), residues: 1103 helix: 1.53 (0.28), residues: 401 sheet: 0.46 (0.30), residues: 300 loop : -0.15 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE A 225 TYR 0.020 0.001 TYR E 178 ARG 0.011 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.94 seconds wall clock time: 70 minutes 23.55 seconds (4223.55 seconds total)