Starting phenix.real_space_refine on Wed Feb 14 00:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y24_33585/02_2024/7y24_33585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y24_33585/02_2024/7y24_33585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y24_33585/02_2024/7y24_33585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y24_33585/02_2024/7y24_33585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y24_33585/02_2024/7y24_33585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y24_33585/02_2024/7y24_33585.pdb" } resolution = 3.25 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= 0.075 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 57 5.16 5 C 5251 2.51 5 N 1381 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "S GLU 222": "OE1" <-> "OE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8229 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1605 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2449 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 117 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 360 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "S" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1722 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Classifications: {'peptide': 8} Modifications used: {'COO': 1, 'PEPT-D': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'DPN%PEPT-D:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2027 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 4.90, per 1000 atoms: 0.60 Number of scatterers: 8229 At special positions: 0 Unit cell: (91.308, 120.657, 125.005, 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 57 16.00 O 1540 8.00 N 1381 7.00 C 5251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN C 1 " pdb=" CB DTR C 4 " Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 15 sheets defined 37.2% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.471A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.577A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 256 removed outlier: 4.126A pdb=" N HIS A 245 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.306A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.695A pdb=" N VAL A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.784A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.930A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 72 Processing helix chain 'E' and resid 76 through 105 Proline residue: E 97 - end of helix removed outlier: 3.626A pdb=" N ALA E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 102 " --> pdb=" O PHE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 146 Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 155 through 180 Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 203 through 219 Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 244 through 282 removed outlier: 4.438A pdb=" N LYS E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 287 through 314 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 316 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 9.228A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.953A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.870A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.676A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.573A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.635A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.738A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 5.256A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.583A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.706A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL S 214 " --> pdb=" O GLN S 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.619A pdb=" N PHE C 3 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 6 " --> pdb=" O PHE C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 182 through 185 457 hydrogen bonds defined for protein. 1323 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: 2.35 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1543 1.33 - 1.45: 2201 1.45 - 1.57: 4584 1.57 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8406 Sorted by residual: bond pdb=" N LEU S 221 " pdb=" CA LEU S 221 " ideal model delta sigma weight residual 1.459 1.401 0.058 1.23e-02 6.61e+03 2.21e+01 bond pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 1.461 1.422 0.039 9.20e-03 1.18e+04 1.82e+01 bond pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 1.520 1.469 0.051 1.23e-02 6.61e+03 1.74e+01 bond pdb=" CA PRO S 224 " pdb=" CB PRO S 224 " ideal model delta sigma weight residual 1.532 1.481 0.051 1.33e-02 5.65e+03 1.49e+01 bond pdb=" CA LEU S 221 " pdb=" C LEU S 221 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.29e-02 6.01e+03 1.04e+01 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.32: 180 106.32 - 113.26: 4634 113.26 - 120.20: 2838 120.20 - 127.15: 3730 127.15 - 134.09: 89 Bond angle restraints: 11471 Sorted by residual: angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 112.75 125.39 -12.64 1.36e+00 5.41e-01 8.63e+01 angle pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " pdb=" CG TYR S 223 " ideal model delta sigma weight residual 113.90 103.75 10.15 1.80e+00 3.09e-01 3.18e+01 angle pdb=" O TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " ideal model delta sigma weight residual 120.48 124.22 -3.74 8.90e-01 1.26e+00 1.76e+01 angle pdb=" N PRO S 224 " pdb=" CA PRO S 224 " pdb=" C PRO S 224 " ideal model delta sigma weight residual 111.03 105.02 6.01 1.54e+00 4.22e-01 1.52e+01 angle pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 120.26 115.51 4.75 1.34e+00 5.57e-01 1.25e+01 ... (remaining 11466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4513 17.95 - 35.91: 303 35.91 - 53.86: 55 53.86 - 71.81: 12 71.81 - 89.77: 5 Dihedral angle restraints: 4888 sinusoidal: 1626 harmonic: 3262 Sorted by residual: dihedral pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual 122.80 147.56 -24.76 0 2.50e+00 1.60e-01 9.81e+01 dihedral pdb=" C TYR S 223 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta harmonic sigma weight residual -122.60 -146.50 23.90 0 2.50e+00 1.60e-01 9.14e+01 dihedral pdb=" CB CYS E 115 " pdb=" SG CYS E 115 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual 93.00 179.61 -86.61 1 1.00e+01 1.00e-02 9.03e+01 ... (remaining 4885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 1353 0.247 - 0.494: 0 0.494 - 0.740: 1 0.740 - 0.987: 0 0.987 - 1.234: 1 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 1.28 1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" CA GLU S 222 " pdb=" N GLU S 222 " pdb=" C GLU S 222 " pdb=" CB GLU S 222 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA LEU S 221 " pdb=" N LEU S 221 " pdb=" C LEU S 221 " pdb=" CB LEU S 221 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1352 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR S 223 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C TYR S 223 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR S 223 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO S 224 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 223 " 0.033 2.00e-02 2.50e+03 2.22e-02 9.89e+00 pdb=" CG TYR S 223 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR S 223 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR S 223 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR S 223 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR S 223 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR S 223 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR S 223 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 164 " 0.018 2.00e-02 2.50e+03 1.52e-02 5.80e+00 pdb=" CG TRP S 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP S 164 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP S 164 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP S 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 164 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 164 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP S 164 " 0.006 2.00e-02 2.50e+03 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 886 2.75 - 3.29: 8456 3.29 - 3.82: 14065 3.82 - 4.36: 15802 4.36 - 4.90: 27828 Nonbonded interactions: 67037 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.208 2.440 nonbonded pdb=" OE2 GLU A 9 " pdb=" ND2 ASN S 157 " model vdw 2.234 2.520 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.249 2.520 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.255 2.440 ... (remaining 67032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 1.760 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.390 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.004 0.058 8406 Z= 0.251 Angle : 0.675 12.637 11471 Z= 0.382 Chirality : 0.057 1.234 1355 Planarity : 0.005 0.055 1453 Dihedral : 12.925 89.767 2777 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.37 % Allowed : 0.25 % Favored : 99.38 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1107 helix: 1.98 (0.26), residues: 389 sheet: -0.01 (0.30), residues: 279 loop : -0.56 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 164 HIS 0.004 0.001 HIS S 35 PHE 0.026 0.002 PHE E 92 TYR 0.045 0.002 TYR S 223 ARG 0.009 0.001 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 305 GLN cc_start: 0.8572 (mt0) cc_final: 0.8117 (tm-30) REVERT: A 313 ARG cc_start: 0.8559 (ttp-170) cc_final: 0.8278 (ttm110) REVERT: A 322 HIS cc_start: 0.7067 (t-90) cc_final: 0.6677 (t-90) REVERT: G 40 TYR cc_start: 0.7716 (t80) cc_final: 0.7312 (t80) REVERT: S 148 ARG cc_start: 0.6574 (ttp80) cc_final: 0.6284 (ttp80) REVERT: S 218 MET cc_start: 0.6506 (mtp) cc_final: 0.6271 (mtp) REVERT: S 222 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: E 122 ASP cc_start: 0.7856 (t70) cc_final: 0.7413 (m-30) outliers start: 3 outliers final: 1 residues processed: 221 average time/residue: 0.1856 time to fit residues: 57.2243 Evaluate side-chains 189 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN E 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8406 Z= 0.270 Angle : 0.585 7.352 11471 Z= 0.310 Chirality : 0.043 0.192 1355 Planarity : 0.004 0.056 1453 Dihedral : 4.814 56.965 1205 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.96 % Allowed : 10.34 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1107 helix: 2.26 (0.25), residues: 392 sheet: -0.07 (0.30), residues: 282 loop : -0.59 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 153 HIS 0.005 0.001 HIS B 54 PHE 0.023 0.002 PHE E 92 TYR 0.026 0.002 TYR S 223 ARG 0.005 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8556 (mt0) cc_final: 0.7957 (tm-30) REVERT: A 313 ARG cc_start: 0.8615 (ttp-170) cc_final: 0.8376 (ttm110) REVERT: B 63 TRP cc_start: 0.8593 (m100) cc_final: 0.8132 (m100) REVERT: G 44 HIS cc_start: 0.7366 (m-70) cc_final: 0.7000 (m170) REVERT: S 113 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7840 (mm-40) outliers start: 24 outliers final: 18 residues processed: 219 average time/residue: 0.1838 time to fit residues: 55.9665 Evaluate side-chains 210 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 308 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS S 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8406 Z= 0.175 Angle : 0.546 6.105 11471 Z= 0.289 Chirality : 0.042 0.218 1355 Planarity : 0.004 0.056 1453 Dihedral : 4.196 25.172 1200 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.71 % Allowed : 14.16 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1107 helix: 2.35 (0.26), residues: 392 sheet: 0.00 (0.30), residues: 281 loop : -0.58 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 197 HIS 0.006 0.001 HIS G 44 PHE 0.020 0.001 PHE E 92 TYR 0.028 0.001 TYR S 223 ARG 0.008 0.001 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8552 (mt0) cc_final: 0.7954 (tm-30) REVERT: A 313 ARG cc_start: 0.8568 (ttp-170) cc_final: 0.8297 (ttm110) REVERT: A 333 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 337 ASP cc_start: 0.8530 (m-30) cc_final: 0.8290 (m-30) REVERT: B 283 ARG cc_start: 0.8053 (tpt170) cc_final: 0.7822 (tpt170) REVERT: S 113 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7953 (mm-40) REVERT: S 223 TYR cc_start: 0.7298 (t80) cc_final: 0.7045 (t80) REVERT: E 139 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7002 (t0) outliers start: 22 outliers final: 14 residues processed: 213 average time/residue: 0.1793 time to fit residues: 53.7320 Evaluate side-chains 202 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 187 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 227 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8406 Z= 0.236 Angle : 0.563 7.762 11471 Z= 0.298 Chirality : 0.043 0.191 1355 Planarity : 0.004 0.057 1453 Dihedral : 4.191 23.402 1200 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.06 % Allowed : 15.02 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1107 helix: 2.23 (0.26), residues: 392 sheet: -0.07 (0.29), residues: 282 loop : -0.52 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 197 HIS 0.004 0.001 HIS B 91 PHE 0.026 0.002 PHE E 92 TYR 0.022 0.001 TYR S 223 ARG 0.004 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLN cc_start: 0.8454 (mt0) cc_final: 0.8135 (tm-30) REVERT: A 313 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.8359 (ttm110) REVERT: A 333 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 283 ARG cc_start: 0.7985 (tpt170) cc_final: 0.7782 (tpt170) REVERT: S 113 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7905 (mm-40) REVERT: S 223 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7465 (t80) REVERT: E 122 ASP cc_start: 0.7740 (t70) cc_final: 0.7271 (m-30) REVERT: E 139 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7051 (t0) outliers start: 33 outliers final: 25 residues processed: 209 average time/residue: 0.1927 time to fit residues: 56.2837 Evaluate side-chains 207 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 227 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8406 Z= 0.297 Angle : 0.603 7.863 11471 Z= 0.320 Chirality : 0.044 0.221 1355 Planarity : 0.004 0.058 1453 Dihedral : 4.347 24.330 1200 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.80 % Allowed : 16.87 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1107 helix: 2.07 (0.26), residues: 391 sheet: -0.14 (0.30), residues: 286 loop : -0.55 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 212 HIS 0.006 0.001 HIS B 91 PHE 0.035 0.002 PHE E 92 TYR 0.028 0.002 TYR E 273 ARG 0.006 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8199 (mp0) cc_final: 0.7841 (mp0) REVERT: A 305 GLN cc_start: 0.8457 (mt0) cc_final: 0.7924 (tm-30) REVERT: A 313 ARG cc_start: 0.8651 (ttp-170) cc_final: 0.8398 (ttm110) REVERT: A 322 HIS cc_start: 0.7155 (t-90) cc_final: 0.6912 (t-90) REVERT: S 36 TRP cc_start: 0.7748 (m100) cc_final: 0.7511 (m100) REVERT: S 113 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7868 (mm-40) REVERT: S 223 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7259 (t80) REVERT: E 139 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7138 (t0) outliers start: 39 outliers final: 32 residues processed: 217 average time/residue: 0.1733 time to fit residues: 53.2346 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8406 Z= 0.346 Angle : 0.638 8.854 11471 Z= 0.339 Chirality : 0.045 0.225 1355 Planarity : 0.004 0.058 1453 Dihedral : 4.520 26.743 1200 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.05 % Allowed : 18.47 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1107 helix: 1.84 (0.25), residues: 391 sheet: -0.31 (0.29), residues: 302 loop : -0.56 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 212 HIS 0.007 0.001 HIS B 91 PHE 0.026 0.002 PHE E 92 TYR 0.020 0.002 TYR E 273 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 198 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8192 (mp0) cc_final: 0.7804 (mp0) REVERT: A 305 GLN cc_start: 0.8614 (mt0) cc_final: 0.8059 (tm-30) REVERT: A 313 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8452 (ttm110) REVERT: A 322 HIS cc_start: 0.7348 (t-90) cc_final: 0.7051 (t-90) REVERT: B 327 VAL cc_start: 0.9011 (t) cc_final: 0.8755 (p) REVERT: S 36 TRP cc_start: 0.7829 (m100) cc_final: 0.7601 (m100) REVERT: S 113 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7893 (mm-40) REVERT: S 223 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.7089 (t80) REVERT: E 139 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7220 (t0) outliers start: 41 outliers final: 29 residues processed: 222 average time/residue: 0.1788 time to fit residues: 55.6819 Evaluate side-chains 222 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.0030 chunk 77 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8406 Z= 0.181 Angle : 0.562 6.891 11471 Z= 0.296 Chirality : 0.042 0.217 1355 Planarity : 0.004 0.059 1453 Dihedral : 4.277 25.747 1200 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.69 % Allowed : 20.94 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1107 helix: 2.13 (0.26), residues: 391 sheet: -0.26 (0.29), residues: 294 loop : -0.45 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 197 HIS 0.003 0.001 HIS E 107 PHE 0.030 0.002 PHE E 92 TYR 0.018 0.001 TYR S 223 ARG 0.008 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8186 (mp0) cc_final: 0.7767 (mp0) REVERT: A 305 GLN cc_start: 0.8486 (mt0) cc_final: 0.8040 (tm-30) REVERT: A 313 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.8386 (ttm110) REVERT: A 322 HIS cc_start: 0.7195 (t-90) cc_final: 0.6872 (t-90) REVERT: B 327 VAL cc_start: 0.8926 (t) cc_final: 0.8690 (p) REVERT: S 36 TRP cc_start: 0.7740 (m100) cc_final: 0.7452 (m100) REVERT: S 67 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5869 (mtm110) REVERT: S 113 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7857 (mm-40) REVERT: E 139 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7050 (t0) outliers start: 30 outliers final: 23 residues processed: 231 average time/residue: 0.1759 time to fit residues: 58.1126 Evaluate side-chains 218 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8406 Z= 0.190 Angle : 0.572 8.110 11471 Z= 0.300 Chirality : 0.042 0.215 1355 Planarity : 0.004 0.058 1453 Dihedral : 4.260 26.741 1200 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.45 % Allowed : 22.29 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1107 helix: 2.09 (0.26), residues: 391 sheet: -0.29 (0.29), residues: 289 loop : -0.48 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 212 HIS 0.003 0.001 HIS E 107 PHE 0.038 0.002 PHE E 92 TYR 0.041 0.002 TYR S 223 ARG 0.011 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8226 (mp0) cc_final: 0.7822 (mp0) REVERT: A 305 GLN cc_start: 0.8510 (mt0) cc_final: 0.8063 (tm-30) REVERT: A 313 ARG cc_start: 0.8624 (ttp-170) cc_final: 0.8375 (ttm110) REVERT: A 322 HIS cc_start: 0.7230 (t-90) cc_final: 0.6905 (t-90) REVERT: B 327 VAL cc_start: 0.8933 (t) cc_final: 0.8700 (p) REVERT: S 36 TRP cc_start: 0.7753 (m100) cc_final: 0.7451 (m100) REVERT: S 113 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7880 (mm-40) REVERT: E 122 ASP cc_start: 0.8058 (t0) cc_final: 0.7344 (m-30) REVERT: E 139 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7012 (t0) outliers start: 28 outliers final: 22 residues processed: 215 average time/residue: 0.1631 time to fit residues: 50.3862 Evaluate side-chains 213 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 194 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 0.0970 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 overall best weight: 1.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8406 Z= 0.238 Angle : 0.598 11.068 11471 Z= 0.313 Chirality : 0.043 0.229 1355 Planarity : 0.004 0.059 1453 Dihedral : 4.259 25.102 1200 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.82 % Allowed : 22.04 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1107 helix: 2.03 (0.26), residues: 392 sheet: -0.31 (0.30), residues: 287 loop : -0.55 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 212 HIS 0.004 0.001 HIS B 91 PHE 0.040 0.002 PHE E 92 TYR 0.031 0.001 TYR S 223 ARG 0.005 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8208 (mp0) cc_final: 0.7822 (mp0) REVERT: A 305 GLN cc_start: 0.8414 (mt0) cc_final: 0.8020 (tm-30) REVERT: A 313 ARG cc_start: 0.8635 (ttp-170) cc_final: 0.8384 (ttm110) REVERT: A 322 HIS cc_start: 0.7315 (t-90) cc_final: 0.7030 (t-90) REVERT: B 327 VAL cc_start: 0.9004 (t) cc_final: 0.8740 (p) REVERT: S 36 TRP cc_start: 0.7729 (m100) cc_final: 0.7402 (m100) REVERT: S 113 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7888 (mm-40) REVERT: E 122 ASP cc_start: 0.8119 (t0) cc_final: 0.7433 (m-30) REVERT: E 139 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7063 (t0) outliers start: 31 outliers final: 27 residues processed: 215 average time/residue: 0.1724 time to fit residues: 53.0073 Evaluate side-chains 220 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 194 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8406 Z= 0.181 Angle : 0.585 10.342 11471 Z= 0.304 Chirality : 0.042 0.227 1355 Planarity : 0.004 0.058 1453 Dihedral : 4.135 25.375 1200 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.20 % Allowed : 22.78 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1107 helix: 2.10 (0.26), residues: 392 sheet: -0.23 (0.30), residues: 284 loop : -0.53 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 212 HIS 0.003 0.001 HIS E 107 PHE 0.031 0.002 PHE E 92 TYR 0.028 0.001 TYR E 302 ARG 0.008 0.001 ARG S 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8202 (mp0) cc_final: 0.7824 (mp0) REVERT: A 305 GLN cc_start: 0.8479 (mt0) cc_final: 0.8112 (tm-30) REVERT: A 313 ARG cc_start: 0.8604 (ttp-170) cc_final: 0.8362 (ttm110) REVERT: A 322 HIS cc_start: 0.7223 (t-90) cc_final: 0.6911 (t-90) REVERT: B 327 VAL cc_start: 0.8950 (t) cc_final: 0.8685 (p) REVERT: G 40 TYR cc_start: 0.8125 (t80) cc_final: 0.7891 (t80) REVERT: S 36 TRP cc_start: 0.7744 (m100) cc_final: 0.7435 (m100) REVERT: S 113 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7863 (mm-40) REVERT: S 164 TRP cc_start: 0.8098 (m100) cc_final: 0.7826 (m100) REVERT: S 233 LEU cc_start: 0.6444 (tt) cc_final: 0.5743 (mp) REVERT: E 122 ASP cc_start: 0.8057 (t0) cc_final: 0.7430 (m-30) REVERT: E 139 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6993 (t0) outliers start: 26 outliers final: 22 residues processed: 220 average time/residue: 0.1609 time to fit residues: 51.2328 Evaluate side-chains 215 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 59 CYS Chi-restraints excluded: chain E residue 107 HIS Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 4 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.184455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147356 restraints weight = 11797.202| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.09 r_work: 0.3711 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8406 Z= 0.197 Angle : 0.591 9.549 11471 Z= 0.308 Chirality : 0.043 0.226 1355 Planarity : 0.004 0.059 1453 Dihedral : 4.115 25.703 1200 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.08 % Allowed : 23.52 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1107 helix: 2.11 (0.26), residues: 392 sheet: -0.26 (0.29), residues: 287 loop : -0.55 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 212 HIS 0.006 0.001 HIS S 35 PHE 0.033 0.002 PHE E 92 TYR 0.025 0.001 TYR E 302 ARG 0.004 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.09 seconds wall clock time: 38 minutes 51.60 seconds (2331.60 seconds total)