Starting phenix.real_space_refine on Wed Feb 14 09:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/02_2024/7ezm_31389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/02_2024/7ezm_31389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/02_2024/7ezm_31389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/02_2024/7ezm_31389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/02_2024/7ezm_31389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/02_2024/7ezm_31389_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.032 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 69 5.16 5 C 5748 2.51 5 N 1524 2.21 5 O 1667 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 ARG 15": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 191": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" 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: 9008 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1850 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2362 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.33, per 1000 atoms: 0.59 Number of scatterers: 9008 At special positions: 0 Unit cell: (104.5, 120.175, 121.22, 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 69 16.00 O 1667 8.00 N 1524 7.00 C 5748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.05 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: 3.69 Conformation dependent library (CDL) restraints added in 1.9 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 35.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 7 through 37 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 235 removed outlier: 3.953A pdb=" N TYR A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.550A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 276 through 284 removed outlier: 4.733A pdb=" N MET A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 302 through 316 removed outlier: 4.347A pdb=" N LEU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 355 removed outlier: 3.903A pdb=" N ILE A 337 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 4.209A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'D' and resid 40 through 68 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 75 through 104 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 144 Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'D' and resid 155 through 179 Proline residue: D 175 - end of helix removed outlier: 3.595A pdb=" N ILE D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 219 through 247 Processing helix chain 'D' and resid 302 through 338 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 350 through 370 removed outlier: 4.019A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.849A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.205A pdb=" N VAL A 269 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS A 327 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 271 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 200 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 42 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG A 202 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 44 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 204 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY A 46 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.882A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.675A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.480A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.814A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.613A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.235A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.631A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 182 through 186 Processing sheet with id= J, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.257A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.476A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 155 through 160 426 hydrogen bonds defined for protein. 1164 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: 2.79 Time building geometry restraints manager: 4.02 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: 2088 1.33 - 1.46: 2829 1.46 - 1.60: 4172 1.60 - 1.73: 1 1.73 - 1.86: 106 Bond restraints: 9196 Sorted by residual: bond pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.462 1.636 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.526 0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.532 1.465 0.066 1.78e-02 3.16e+03 1.39e+01 bond pdb=" N VAL A 240 " pdb=" CA VAL A 240 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.60e+00 bond pdb=" N GLY B 41 " pdb=" CA GLY B 41 " ideal model delta sigma weight residual 1.448 1.492 -0.044 1.88e-02 2.83e+03 5.56e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.24: 169 105.24 - 112.62: 4599 112.62 - 120.01: 3548 120.01 - 127.39: 4068 127.39 - 134.78: 100 Bond angle restraints: 12484 Sorted by residual: angle pdb=" C ARG D 139 " pdb=" CA ARG D 139 " pdb=" CB ARG D 139 " ideal model delta sigma weight residual 110.68 118.72 -8.04 1.70e+00 3.46e-01 2.23e+01 angle pdb=" C ARG D 345 " pdb=" CA ARG D 345 " pdb=" CB ARG D 345 " ideal model delta sigma weight residual 110.88 103.83 7.05 1.57e+00 4.06e-01 2.02e+01 angle pdb=" N VAL A 238 " pdb=" CA VAL A 238 " pdb=" C VAL A 238 " ideal model delta sigma weight residual 109.20 102.41 6.79 1.55e+00 4.16e-01 1.92e+01 angle pdb=" N ALA H 136 " pdb=" CA ALA H 136 " pdb=" C ALA H 136 " ideal model delta sigma weight residual 113.02 107.99 5.03 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA VAL A 238 " pdb=" C VAL A 238 " pdb=" O VAL A 238 " ideal model delta sigma weight residual 121.92 117.04 4.88 1.17e+00 7.31e-01 1.74e+01 ... (remaining 12479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4939 16.36 - 32.71: 413 32.71 - 49.06: 76 49.06 - 65.42: 22 65.42 - 81.77: 5 Dihedral angle restraints: 5455 sinusoidal: 2051 harmonic: 3404 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1137 0.081 - 0.163: 272 0.163 - 0.244: 23 0.244 - 0.325: 3 0.325 - 0.407: 2 Chirality restraints: 1437 Sorted by residual: chirality pdb=" CA ARG A 210 " pdb=" N ARG A 210 " pdb=" C ARG A 210 " pdb=" CB ARG A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA ARG D 345 " pdb=" N ARG D 345 " pdb=" C ARG D 345 " pdb=" CB ARG D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1434 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 313 " 0.048 9.50e-02 1.11e+02 4.23e-02 1.69e+01 pdb=" NE ARG D 313 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG D 313 " 0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG D 313 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG D 313 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 367 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PRO D 367 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO D 367 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE D 368 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 202 " -0.006 9.50e-02 1.11e+02 3.17e-02 1.25e+01 pdb=" NE ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 202 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 202 " 0.020 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1306 2.76 - 3.30: 9258 3.30 - 3.83: 15488 3.83 - 4.37: 19207 4.37 - 4.90: 32183 Nonbonded interactions: 77442 Sorted by model distance: nonbonded pdb=" OH TYR A 356 " pdb=" OE1 GLN D 153 " model vdw 2.228 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 2.440 nonbonded pdb=" O TYR D 360 " pdb=" OG SER D 363 " model vdw 2.247 2.440 nonbonded pdb=" O MET D 72 " pdb=" ND2 ASN D 77 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.260 2.440 ... (remaining 77437 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.180 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.160 Find NCS groups from input model: 0.280 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.011 0.174 9196 Z= 0.698 Angle : 1.074 9.054 12484 Z= 0.645 Chirality : 0.068 0.407 1437 Planarity : 0.009 0.102 1576 Dihedral : 13.160 81.772 3241 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.94 % Allowed : 3.34 % Favored : 95.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % 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 (0.23), residues: 1150 helix: -0.43 (0.23), residues: 404 sheet: -0.10 (0.30), residues: 278 loop : -0.83 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP B 82 HIS 0.019 0.006 HIS D 157 PHE 0.025 0.006 PHE B 241 TYR 0.046 0.009 TYR H 175 ARG 0.071 0.009 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 308 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.7426 (p) cc_final: 0.6994 (p) REVERT: A 9 ASP cc_start: 0.6886 (m-30) cc_final: 0.6420 (m-30) REVERT: A 39 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 237 GLN cc_start: 0.7324 (mt0) cc_final: 0.7086 (mt0) REVERT: A 275 LYS cc_start: 0.7832 (mttt) cc_final: 0.7625 (mttt) REVERT: B 67 SER cc_start: 0.7986 (m) cc_final: 0.7689 (t) REVERT: B 74 SER cc_start: 0.7782 (t) cc_final: 0.7454 (t) REVERT: B 98 SER cc_start: 0.7826 (p) cc_final: 0.7445 (t) REVERT: B 118 ASP cc_start: 0.6246 (p0) cc_final: 0.5987 (p0) REVERT: B 184 THR cc_start: 0.8506 (p) cc_final: 0.8296 (t) REVERT: B 220 GLN cc_start: 0.8247 (mt0) cc_final: 0.7890 (mt0) REVERT: B 221 THR cc_start: 0.7915 (m) cc_final: 0.7714 (t) REVERT: B 277 SER cc_start: 0.8359 (t) cc_final: 0.8149 (t) REVERT: B 334 SER cc_start: 0.7768 (m) cc_final: 0.7554 (p) REVERT: D 76 THR cc_start: 0.7375 (m) cc_final: 0.7143 (m) REVERT: D 111 SER cc_start: 0.8252 (t) cc_final: 0.8007 (p) REVERT: H 141 THR cc_start: 0.7753 (m) cc_final: 0.7420 (p) REVERT: H 180 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7688 (mtt180) outliers start: 9 outliers final: 4 residues processed: 315 average time/residue: 1.0506 time to fit residues: 354.4163 Evaluate side-chains 277 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN D 374 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9196 Z= 0.208 Angle : 0.599 6.607 12484 Z= 0.315 Chirality : 0.044 0.149 1437 Planarity : 0.005 0.048 1576 Dihedral : 6.806 72.639 1271 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.91 % Allowed : 13.47 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.53 (0.25), residues: 1150 helix: 1.28 (0.26), residues: 408 sheet: -0.14 (0.30), residues: 272 loop : -0.01 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS B 62 PHE 0.032 0.002 PHE A 55 TYR 0.012 0.002 TYR D 179 ARG 0.008 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 266 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.7768 (p) cc_final: 0.7536 (p) REVERT: A 9 ASP cc_start: 0.6998 (m-30) cc_final: 0.6616 (m-30) REVERT: A 39 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6713 (mt-10) REVERT: A 201 PHE cc_start: 0.8214 (m-80) cc_final: 0.7686 (m-80) REVERT: B 52 ARG cc_start: 0.7070 (ttm110) cc_final: 0.6841 (mtm-85) REVERT: B 98 SER cc_start: 0.7635 (p) cc_final: 0.7249 (t) REVERT: B 137 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7619 (tpp-160) REVERT: B 161 SER cc_start: 0.7208 (m) cc_final: 0.6952 (p) REVERT: B 170 ASP cc_start: 0.7021 (t70) cc_final: 0.6754 (t0) REVERT: B 220 GLN cc_start: 0.8102 (mt0) cc_final: 0.7891 (mt0) REVERT: B 268 ASN cc_start: 0.7324 (p0) cc_final: 0.7083 (p0) REVERT: B 289 TYR cc_start: 0.7229 (m-10) cc_final: 0.6859 (m-80) REVERT: D 126 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8095 (m) REVERT: D 202 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7051 (p0) REVERT: D 308 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7873 (mttm) REVERT: D 344 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7201 (mt-10) REVERT: H 68 PHE cc_start: 0.6968 (m-10) cc_final: 0.6742 (m-80) REVERT: H 78 THR cc_start: 0.8447 (t) cc_final: 0.7883 (m) REVERT: H 141 THR cc_start: 0.7815 (m) cc_final: 0.7475 (p) REVERT: H 180 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7678 (mtt180) outliers start: 47 outliers final: 23 residues processed: 285 average time/residue: 1.0838 time to fit residues: 330.9302 Evaluate side-chains 274 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 249 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN D 374 ASN H 39 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9196 Z= 0.218 Angle : 0.565 6.460 12484 Z= 0.294 Chirality : 0.043 0.143 1437 Planarity : 0.004 0.051 1576 Dihedral : 5.364 69.500 1263 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.28 % Allowed : 17.54 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1150 helix: 1.41 (0.26), residues: 412 sheet: -0.12 (0.29), residues: 288 loop : 0.12 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.005 0.001 HIS B 62 PHE 0.027 0.002 PHE A 55 TYR 0.015 0.001 TYR D 179 ARG 0.009 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 261 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.7866 (p) cc_final: 0.7562 (p) REVERT: A 9 ASP cc_start: 0.6956 (m-30) cc_final: 0.6635 (m-30) REVERT: A 17 LYS cc_start: 0.7768 (mttm) cc_final: 0.7563 (mmtp) REVERT: A 39 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6668 (mt-10) REVERT: A 201 PHE cc_start: 0.8303 (m-80) cc_final: 0.7655 (m-80) REVERT: A 247 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6762 (mtm-85) REVERT: A 307 GLU cc_start: 0.7355 (tp30) cc_final: 0.7103 (tp30) REVERT: B 52 ARG cc_start: 0.7144 (ttm110) cc_final: 0.6900 (mtp85) REVERT: B 98 SER cc_start: 0.7846 (p) cc_final: 0.7514 (t) REVERT: B 137 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7621 (tpp-160) REVERT: B 170 ASP cc_start: 0.7083 (t70) cc_final: 0.6744 (t0) REVERT: B 212 ASP cc_start: 0.7165 (t70) cc_final: 0.6945 (t0) REVERT: B 220 GLN cc_start: 0.8084 (mt0) cc_final: 0.7679 (mt0) REVERT: D 126 SER cc_start: 0.8394 (t) cc_final: 0.8112 (m) REVERT: D 202 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7287 (p0) REVERT: D 308 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7877 (mttm) REVERT: D 329 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7966 (tt) outliers start: 41 outliers final: 20 residues processed: 278 average time/residue: 1.1161 time to fit residues: 331.8931 Evaluate side-chains 275 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 304 ASN D 366 ASN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9196 Z= 0.274 Angle : 0.571 6.919 12484 Z= 0.296 Chirality : 0.043 0.156 1437 Planarity : 0.004 0.051 1576 Dihedral : 5.281 69.462 1262 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.91 % Allowed : 19.31 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1150 helix: 1.50 (0.26), residues: 407 sheet: -0.20 (0.29), residues: 285 loop : 0.08 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.045 0.002 PHE H 68 TYR 0.016 0.002 TYR D 179 ARG 0.010 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8004 (p) cc_final: 0.7801 (p) REVERT: A 9 ASP cc_start: 0.7042 (m-30) cc_final: 0.6726 (m-30) REVERT: A 10 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7988 (mtmm) REVERT: A 17 LYS cc_start: 0.7790 (mttm) cc_final: 0.7564 (mmtp) REVERT: A 39 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 201 PHE cc_start: 0.8354 (m-80) cc_final: 0.7678 (m-80) REVERT: A 237 GLN cc_start: 0.7316 (mt0) cc_final: 0.6966 (mt0) REVERT: A 247 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6742 (mtm-85) REVERT: A 307 GLU cc_start: 0.7426 (tp30) cc_final: 0.7102 (tp30) REVERT: A 326 SER cc_start: 0.8260 (p) cc_final: 0.7943 (t) REVERT: B 52 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6919 (ptp90) REVERT: B 98 SER cc_start: 0.7939 (p) cc_final: 0.7541 (t) REVERT: B 137 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7604 (tpp-160) REVERT: B 170 ASP cc_start: 0.7121 (t70) cc_final: 0.6853 (t0) REVERT: B 184 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8126 (p) REVERT: B 212 ASP cc_start: 0.7201 (t70) cc_final: 0.6991 (t0) REVERT: B 220 GLN cc_start: 0.8095 (mt0) cc_final: 0.7814 (mt0) REVERT: B 268 ASN cc_start: 0.7637 (p0) cc_final: 0.7346 (p0) REVERT: B 312 ASP cc_start: 0.6839 (t0) cc_final: 0.6624 (t70) REVERT: D 74 THR cc_start: 0.7986 (t) cc_final: 0.7534 (p) REVERT: D 126 SER cc_start: 0.8405 (t) cc_final: 0.8163 (m) REVERT: D 202 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7348 (p0) REVERT: D 241 LYS cc_start: 0.7530 (mttp) cc_final: 0.7324 (mttp) REVERT: D 308 LYS cc_start: 0.8117 (mmtp) cc_final: 0.7881 (mttp) REVERT: D 329 ILE cc_start: 0.8167 (tp) cc_final: 0.7962 (tt) REVERT: D 336 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7612 (ttt180) REVERT: H 20 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7484 (pp) REVERT: H 63 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (t) REVERT: H 67 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7504 (ttp80) REVERT: H 68 PHE cc_start: 0.7361 (m-10) cc_final: 0.6998 (m-10) outliers start: 47 outliers final: 20 residues processed: 279 average time/residue: 1.2146 time to fit residues: 360.6084 Evaluate side-chains 269 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 131 ASN D 304 ASN D 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9196 Z= 0.234 Angle : 0.552 7.361 12484 Z= 0.285 Chirality : 0.043 0.168 1437 Planarity : 0.004 0.055 1576 Dihedral : 5.214 70.244 1262 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.01 % Allowed : 19.10 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.63 (0.25), residues: 1150 helix: 1.55 (0.26), residues: 409 sheet: -0.26 (0.29), residues: 286 loop : -0.02 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.026 0.002 PHE H 68 TYR 0.015 0.001 TYR D 179 ARG 0.015 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 251 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.7991 (p) cc_final: 0.7730 (p) REVERT: A 9 ASP cc_start: 0.7022 (m-30) cc_final: 0.6698 (m-30) REVERT: A 10 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7972 (mtmm) REVERT: A 17 LYS cc_start: 0.7787 (mttm) cc_final: 0.7563 (mmtp) REVERT: A 39 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6622 (mt-10) REVERT: A 201 PHE cc_start: 0.8398 (m-80) cc_final: 0.7657 (m-80) REVERT: A 237 GLN cc_start: 0.7297 (mt0) cc_final: 0.6973 (mt0) REVERT: A 247 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6792 (mtm-85) REVERT: A 307 GLU cc_start: 0.7428 (tp30) cc_final: 0.7109 (tp30) REVERT: A 326 SER cc_start: 0.8254 (p) cc_final: 0.7950 (t) REVERT: B 52 ARG cc_start: 0.7152 (ttm110) cc_final: 0.6901 (mtp85) REVERT: B 98 SER cc_start: 0.7903 (p) cc_final: 0.7488 (t) REVERT: B 170 ASP cc_start: 0.7145 (t70) cc_final: 0.6850 (t0) REVERT: B 212 ASP cc_start: 0.7192 (t70) cc_final: 0.6987 (t0) REVERT: B 220 GLN cc_start: 0.8080 (mt0) cc_final: 0.7773 (mt0) REVERT: B 268 ASN cc_start: 0.7659 (p0) cc_final: 0.7441 (p0) REVERT: B 286 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 312 ASP cc_start: 0.6827 (t0) cc_final: 0.6617 (t70) REVERT: D 74 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7545 (p) REVERT: D 75 VAL cc_start: 0.7943 (p) cc_final: 0.7559 (t) REVERT: D 126 SER cc_start: 0.8392 (t) cc_final: 0.8120 (m) REVERT: D 202 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7407 (p0) REVERT: D 241 LYS cc_start: 0.7531 (mttp) cc_final: 0.7309 (mttp) REVERT: D 308 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7884 (mttp) REVERT: D 323 PHE cc_start: 0.8300 (m-80) cc_final: 0.7954 (m-80) REVERT: D 329 ILE cc_start: 0.8156 (tp) cc_final: 0.7954 (tt) REVERT: H 67 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7354 (ttp80) REVERT: H 90 ASP cc_start: 0.8012 (m-30) cc_final: 0.7760 (m-30) outliers start: 48 outliers final: 21 residues processed: 275 average time/residue: 1.1360 time to fit residues: 333.9818 Evaluate side-chains 274 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 249 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 44 GLN D 304 ASN D 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9196 Z= 0.304 Angle : 0.576 9.649 12484 Z= 0.297 Chirality : 0.044 0.156 1437 Planarity : 0.005 0.063 1576 Dihedral : 5.284 69.996 1262 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.32 % Allowed : 18.79 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.53 (0.25), residues: 1150 helix: 1.53 (0.26), residues: 408 sheet: -0.34 (0.28), residues: 290 loop : -0.13 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.005 0.001 HIS B 62 PHE 0.025 0.002 PHE A 55 TYR 0.025 0.002 TYR H 190 ARG 0.016 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 255 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7051 (m-30) cc_final: 0.6752 (m-30) REVERT: A 10 LYS cc_start: 0.8269 (mtmm) cc_final: 0.8047 (mtmm) REVERT: A 39 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6608 (mt-10) REVERT: A 201 PHE cc_start: 0.8422 (m-80) cc_final: 0.7708 (m-80) REVERT: A 237 GLN cc_start: 0.7304 (mt0) cc_final: 0.6936 (mt0) REVERT: A 247 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6798 (mtm-85) REVERT: A 294 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 307 GLU cc_start: 0.7421 (tp30) cc_final: 0.7109 (tp30) REVERT: A 326 SER cc_start: 0.8271 (p) cc_final: 0.7981 (t) REVERT: B 52 ARG cc_start: 0.7267 (ttm110) cc_final: 0.7022 (mtp85) REVERT: B 98 SER cc_start: 0.8046 (p) cc_final: 0.7720 (t) REVERT: B 170 ASP cc_start: 0.7181 (t70) cc_final: 0.6890 (t0) REVERT: B 212 ASP cc_start: 0.7210 (t70) cc_final: 0.7007 (t0) REVERT: B 220 GLN cc_start: 0.8124 (mt0) cc_final: 0.7814 (mt0) REVERT: B 268 ASN cc_start: 0.7606 (p0) cc_final: 0.7401 (p0) REVERT: B 286 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 312 ASP cc_start: 0.6872 (t0) cc_final: 0.6662 (t70) REVERT: D 75 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7716 (t) REVERT: D 126 SER cc_start: 0.8405 (t) cc_final: 0.8152 (m) REVERT: D 202 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7480 (p0) REVERT: D 241 LYS cc_start: 0.7548 (mttp) cc_final: 0.7326 (mttp) REVERT: D 323 PHE cc_start: 0.8283 (m-80) cc_final: 0.7911 (m-80) REVERT: D 329 ILE cc_start: 0.8156 (tp) cc_final: 0.7954 (tt) REVERT: D 336 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7620 (ttt180) REVERT: H 68 PHE cc_start: 0.7130 (m-10) cc_final: 0.6824 (m-10) outliers start: 51 outliers final: 26 residues processed: 275 average time/residue: 1.1472 time to fit residues: 336.6110 Evaluate side-chains 285 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 254 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 230 ASN D 304 ASN D 374 ASN H 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9196 Z= 0.227 Angle : 0.562 9.371 12484 Z= 0.286 Chirality : 0.042 0.155 1437 Planarity : 0.004 0.062 1576 Dihedral : 5.258 70.126 1262 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.01 % Allowed : 20.04 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.56 (0.25), residues: 1150 helix: 1.65 (0.26), residues: 405 sheet: -0.38 (0.29), residues: 285 loop : -0.15 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.002 PHE D 109 TYR 0.030 0.002 TYR H 190 ARG 0.015 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 259 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7997 (mtmm) REVERT: A 39 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6590 (mt-10) REVERT: A 237 GLN cc_start: 0.7299 (mt0) cc_final: 0.6952 (mt0) REVERT: A 247 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6766 (mtm-85) REVERT: A 294 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 307 GLU cc_start: 0.7387 (tp30) cc_final: 0.7076 (tp30) REVERT: A 326 SER cc_start: 0.8239 (p) cc_final: 0.7966 (t) REVERT: B 52 ARG cc_start: 0.7123 (ttm110) cc_final: 0.6900 (ptp90) REVERT: B 98 SER cc_start: 0.8042 (p) cc_final: 0.7659 (t) REVERT: B 170 ASP cc_start: 0.7169 (t70) cc_final: 0.6851 (t0) REVERT: B 212 ASP cc_start: 0.7208 (t70) cc_final: 0.6996 (t0) REVERT: B 220 GLN cc_start: 0.8136 (mt0) cc_final: 0.7813 (mt0) REVERT: B 286 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7920 (mp) REVERT: B 312 ASP cc_start: 0.6850 (t0) cc_final: 0.6642 (t70) REVERT: D 75 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7711 (t) REVERT: D 126 SER cc_start: 0.8387 (t) cc_final: 0.8159 (m) REVERT: D 202 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7426 (p0) REVERT: D 227 VAL cc_start: 0.8169 (t) cc_final: 0.7947 (m) REVERT: D 241 LYS cc_start: 0.7514 (mttp) cc_final: 0.7287 (mttp) REVERT: D 308 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7867 (mttm) REVERT: D 323 PHE cc_start: 0.8309 (m-80) cc_final: 0.7924 (m-80) REVERT: D 329 ILE cc_start: 0.8141 (tp) cc_final: 0.7934 (tt) REVERT: D 336 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7605 (ttt180) REVERT: H 17 SER cc_start: 0.7596 (m) cc_final: 0.7390 (t) REVERT: H 67 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7595 (ttp80) REVERT: H 83 MET cc_start: 0.7944 (mtm) cc_final: 0.7711 (mtm) outliers start: 48 outliers final: 27 residues processed: 282 average time/residue: 1.2879 time to fit residues: 385.9276 Evaluate side-chains 288 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 256 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 304 ASN D 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9196 Z= 0.241 Angle : 0.574 11.280 12484 Z= 0.292 Chirality : 0.043 0.166 1437 Planarity : 0.005 0.055 1576 Dihedral : 5.231 69.729 1262 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.18 % Allowed : 21.71 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.53 (0.25), residues: 1150 helix: 1.63 (0.26), residues: 406 sheet: -0.37 (0.29), residues: 279 loop : -0.20 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.018 0.002 PHE D 109 TYR 0.034 0.002 TYR H 190 ARG 0.014 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8237 (mtmm) cc_final: 0.8034 (mtmm) REVERT: A 39 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6593 (mt-10) REVERT: A 237 GLN cc_start: 0.7310 (mt0) cc_final: 0.7032 (mt0) REVERT: A 247 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6798 (mtm-85) REVERT: A 307 GLU cc_start: 0.7373 (tp30) cc_final: 0.7062 (tp30) REVERT: A 326 SER cc_start: 0.8252 (p) cc_final: 0.7974 (t) REVERT: B 52 ARG cc_start: 0.7190 (ttm110) cc_final: 0.6988 (ptp90) REVERT: B 98 SER cc_start: 0.8053 (p) cc_final: 0.7701 (t) REVERT: B 137 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7561 (tpp-160) REVERT: B 170 ASP cc_start: 0.7156 (t70) cc_final: 0.6830 (t0) REVERT: B 212 ASP cc_start: 0.7211 (t70) cc_final: 0.7006 (t0) REVERT: B 220 GLN cc_start: 0.8145 (mt0) cc_final: 0.7834 (mt0) REVERT: B 286 LEU cc_start: 0.8224 (mp) cc_final: 0.8022 (mp) REVERT: B 312 ASP cc_start: 0.6860 (t0) cc_final: 0.6659 (t70) REVERT: D 75 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7722 (t) REVERT: D 126 SER cc_start: 0.8427 (t) cc_final: 0.8179 (m) REVERT: D 202 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7449 (p0) REVERT: D 227 VAL cc_start: 0.8248 (t) cc_final: 0.7994 (m) REVERT: D 241 LYS cc_start: 0.7503 (mttp) cc_final: 0.7258 (mttp) REVERT: D 308 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7861 (mttp) REVERT: D 323 PHE cc_start: 0.8281 (m-80) cc_final: 0.7928 (m-80) REVERT: D 329 ILE cc_start: 0.8144 (tp) cc_final: 0.7936 (tt) REVERT: D 336 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7601 (ttt180) REVERT: H 17 SER cc_start: 0.7619 (m) cc_final: 0.7370 (t) REVERT: H 67 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7583 (ttp80) REVERT: H 83 MET cc_start: 0.7940 (mtm) cc_final: 0.7720 (mtm) REVERT: H 194 ASN cc_start: 0.8067 (m-40) cc_final: 0.7794 (m-40) outliers start: 40 outliers final: 28 residues processed: 276 average time/residue: 1.3597 time to fit residues: 398.5696 Evaluate side-chains 282 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 107 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 304 ASN D 366 ASN D 374 ASN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9196 Z= 0.188 Angle : 0.556 10.532 12484 Z= 0.283 Chirality : 0.042 0.167 1437 Planarity : 0.004 0.052 1576 Dihedral : 5.078 70.273 1262 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.55 % Allowed : 22.65 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.55 (0.25), residues: 1150 helix: 1.68 (0.26), residues: 406 sheet: -0.40 (0.29), residues: 280 loop : -0.20 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 62 PHE 0.018 0.002 PHE D 109 TYR 0.032 0.002 TYR H 190 ARG 0.012 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7300 (mt0) cc_final: 0.7056 (mt0) REVERT: A 247 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6710 (mtm-85) REVERT: A 252 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7856 (mtpm) REVERT: A 307 GLU cc_start: 0.7385 (tp30) cc_final: 0.7068 (tp30) REVERT: A 326 SER cc_start: 0.8223 (p) cc_final: 0.7958 (t) REVERT: B 98 SER cc_start: 0.8008 (p) cc_final: 0.7584 (t) REVERT: B 137 ARG cc_start: 0.7769 (tpp-160) cc_final: 0.7564 (tpp-160) REVERT: B 170 ASP cc_start: 0.7092 (t70) cc_final: 0.6749 (t0) REVERT: B 220 GLN cc_start: 0.8149 (mt0) cc_final: 0.7827 (mt0) REVERT: D 75 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7661 (t) REVERT: D 126 SER cc_start: 0.8408 (t) cc_final: 0.8169 (m) REVERT: D 202 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7426 (p0) REVERT: D 227 VAL cc_start: 0.8246 (t) cc_final: 0.8028 (m) REVERT: D 241 LYS cc_start: 0.7461 (mttp) cc_final: 0.7192 (mttp) REVERT: D 308 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7869 (mttp) REVERT: D 323 PHE cc_start: 0.8255 (m-80) cc_final: 0.7950 (m-80) REVERT: D 329 ILE cc_start: 0.8127 (tp) cc_final: 0.7920 (tt) REVERT: H 67 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7655 (ttp80) REVERT: H 83 MET cc_start: 0.7936 (mtm) cc_final: 0.7716 (mtm) REVERT: H 194 ASN cc_start: 0.7979 (m-40) cc_final: 0.7765 (m-40) outliers start: 34 outliers final: 25 residues processed: 270 average time/residue: 1.3395 time to fit residues: 383.6015 Evaluate side-chains 282 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 254 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN D 304 ASN D 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9196 Z= 0.225 Angle : 0.571 10.025 12484 Z= 0.290 Chirality : 0.043 0.173 1437 Planarity : 0.005 0.058 1576 Dihedral : 5.077 69.748 1262 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.13 % Allowed : 23.59 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.51 (0.25), residues: 1150 helix: 1.68 (0.26), residues: 406 sheet: -0.44 (0.29), residues: 283 loop : -0.23 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.002 PHE A 55 TYR 0.029 0.002 TYR H 190 ARG 0.015 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 256 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7333 (mt0) cc_final: 0.7068 (mt0) REVERT: A 247 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6811 (mtm-85) REVERT: A 252 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7837 (mtpm) REVERT: A 307 GLU cc_start: 0.7395 (tp30) cc_final: 0.7081 (tp30) REVERT: A 326 SER cc_start: 0.8237 (p) cc_final: 0.7975 (t) REVERT: B 98 SER cc_start: 0.8064 (p) cc_final: 0.7706 (t) REVERT: B 137 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7572 (tpp-160) REVERT: B 170 ASP cc_start: 0.7084 (t70) cc_final: 0.6775 (t0) REVERT: B 220 GLN cc_start: 0.8154 (mt0) cc_final: 0.7826 (mt0) REVERT: D 75 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7639 (t) REVERT: D 126 SER cc_start: 0.8395 (t) cc_final: 0.8154 (m) REVERT: D 202 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7423 (p0) REVERT: D 227 VAL cc_start: 0.8256 (t) cc_final: 0.8025 (m) REVERT: D 241 LYS cc_start: 0.7461 (mttp) cc_final: 0.7196 (mttp) REVERT: D 308 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7861 (mttp) REVERT: D 323 PHE cc_start: 0.8272 (m-80) cc_final: 0.7960 (m-80) REVERT: D 329 ILE cc_start: 0.8128 (tp) cc_final: 0.7919 (tt) REVERT: H 67 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7597 (ttp80) outliers start: 30 outliers final: 22 residues processed: 269 average time/residue: 1.2747 time to fit residues: 363.6649 Evaluate side-chains 277 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 252 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 304 ASN D 374 ASN H 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116521 restraints weight = 12038.239| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.87 r_work: 0.3353 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9196 Z= 0.211 Angle : 0.574 9.640 12484 Z= 0.289 Chirality : 0.042 0.154 1437 Planarity : 0.005 0.059 1576 Dihedral : 5.042 69.500 1262 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.03 % Allowed : 24.53 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.52 (0.25), residues: 1150 helix: 1.70 (0.26), residues: 406 sheet: -0.42 (0.29), residues: 283 loop : -0.25 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE A 55 TYR 0.015 0.002 TYR B 289 ARG 0.013 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5182.86 seconds wall clock time: 92 minutes 8.16 seconds (5528.16 seconds total)