Starting phenix.real_space_refine on Sat Aug 3 20:48:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/08_2024/7ezm_31389.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/08_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_31389/08_2024/7ezm_31389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/08_2024/7ezm_31389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/08_2024/7ezm_31389.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezm_31389/08_2024/7ezm_31389.cif" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.59, per 1000 atoms: 0.62 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: 3.90 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 31 helices and 13 sheets defined 40.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.595A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.550A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN A 266 " --> pdb=" O TRP A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 6 through 26 removed outlier: 4.209A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'D' and resid 39 through 69 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 74 through 105 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 110 through 145 Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 154 through 173 Processing helix chain 'D' and resid 174 through 180 removed outlier: 3.595A pdb=" N ILE D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 218 through 248 Processing helix chain 'D' and resid 301 through 339 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 349 through 371 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 374 through 383 Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.849A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52 through 56 removed outlier: 4.106A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 6.662A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, 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: 6.232A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, 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: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.354A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (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=AA6, 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=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.827A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (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=AA9, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.063A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.507A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1335 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: 2.61 Time building geometry restraints manager: 4.32 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: 1292 2.76 - 3.30: 9206 3.30 - 3.83: 15416 3.83 - 4.37: 19126 4.37 - 4.90: 32178 Nonbonded interactions: 77218 Sorted by model distance: nonbonded pdb=" OH TYR A 356 " pdb=" OE1 GLN D 153 " model vdw 2.228 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 3.040 nonbonded pdb=" O TYR D 360 " pdb=" OG SER D 363 " model vdw 2.247 3.040 nonbonded pdb=" O MET D 72 " pdb=" ND2 ASN D 77 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.260 3.040 ... (remaining 77213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.510 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.950 ------------------------------------------------------------------------------- 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= 0.684 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 : 1.006 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: 1.0465 time to fit residues: 353.5709 Evaluate side-chains 277 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.0170 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN D 131 ASN D 374 ASN H 142 GLN H 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9196 Z= 0.232 Angle : 0.620 6.811 12484 Z= 0.329 Chirality : 0.045 0.164 1437 Planarity : 0.004 0.042 1576 Dihedral : 6.901 72.494 1271 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.70 % Allowed : 13.36 % Favored : 81.94 % 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: 1.35 (0.26), residues: 409 sheet: -0.23 (0.29), residues: 282 loop : 0.02 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.005 0.001 HIS B 62 PHE 0.033 0.002 PHE A 55 TYR 0.014 0.002 TYR H 190 ARG 0.008 0.001 ARG D 345 *********************** 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 317 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 272 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8104 (p) cc_final: 0.7793 (p) REVERT: A 39 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6707 (mt-10) REVERT: A 201 PHE cc_start: 0.8170 (m-80) cc_final: 0.7659 (m-80) REVERT: A 212 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6776 (mt-10) REVERT: A 276 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7026 (ptpp) REVERT: B 68 ARG cc_start: 0.7989 (ttt180) cc_final: 0.7705 (ttt180) REVERT: B 98 SER cc_start: 0.7520 (p) cc_final: 0.7143 (t) REVERT: B 170 ASP cc_start: 0.7163 (t70) cc_final: 0.6842 (OUTLIER) REVERT: B 268 ASN cc_start: 0.7336 (p0) cc_final: 0.7087 (p0) REVERT: D 77 ASN cc_start: 0.8023 (m-40) cc_final: 0.7741 (m-40) REVERT: D 85 VAL cc_start: 0.8209 (t) cc_final: 0.7976 (p) REVERT: D 126 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8108 (m) REVERT: D 202 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7137 (p0) REVERT: D 308 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7891 (mttm) REVERT: D 344 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7218 (mt-10) REVERT: H 34 MET cc_start: 0.8056 (mmt) cc_final: 0.7851 (mmm) REVERT: H 68 PHE cc_start: 0.6982 (m-10) cc_final: 0.6768 (m-80) REVERT: H 78 THR cc_start: 0.8452 (t) cc_final: 0.7871 (m) REVERT: H 141 THR cc_start: 0.7823 (m) cc_final: 0.7537 (p) REVERT: H 180 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7856 (mtt180) outliers start: 45 outliers final: 23 residues processed: 290 average time/residue: 1.0943 time to fit residues: 339.5466 Evaluate side-chains 262 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 196 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL 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 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: 2.9990 chunk 85 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 101 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 ASN G 18 GLN H 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2896 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= 0.226 Angle : 0.578 7.512 12484 Z= 0.303 Chirality : 0.043 0.153 1437 Planarity : 0.004 0.042 1576 Dihedral : 5.521 69.557 1263 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.38 % Allowed : 16.91 % Favored : 78.71 % 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: 0.70 (0.25), residues: 1150 helix: 1.59 (0.25), residues: 417 sheet: -0.22 (0.29), residues: 280 loop : -0.01 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.004 0.001 HIS G 44 PHE 0.032 0.002 PHE A 55 TYR 0.016 0.001 TYR D 179 ARG 0.008 0.001 ARG B 129 *********************** 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 299 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 257 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8273 (p) cc_final: 0.7929 (p) REVERT: A 9 ASP cc_start: 0.7229 (m-30) cc_final: 0.6874 (m-30) REVERT: A 39 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6695 (mt-10) REVERT: A 201 PHE cc_start: 0.8272 (m-80) cc_final: 0.7695 (m-80) REVERT: A 227 MET cc_start: 0.7226 (mtp) cc_final: 0.6981 (mtp) REVERT: A 276 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7139 (ptpp) REVERT: A 307 GLU cc_start: 0.7404 (tp30) cc_final: 0.7121 (tp30) REVERT: A 326 SER cc_start: 0.8289 (p) cc_final: 0.8044 (t) REVERT: B 87 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7590 (t) REVERT: B 98 SER cc_start: 0.7731 (p) cc_final: 0.7412 (t) REVERT: B 170 ASP cc_start: 0.7336 (t70) cc_final: 0.7000 (t0) REVERT: B 191 SER cc_start: 0.7935 (p) cc_final: 0.7733 (p) REVERT: B 227 SER cc_start: 0.8200 (t) cc_final: 0.7821 (t) REVERT: B 268 ASN cc_start: 0.7388 (p0) cc_final: 0.7174 (OUTLIER) REVERT: B 274 THR cc_start: 0.7694 (m) cc_final: 0.7426 (p) REVERT: D 126 SER cc_start: 0.8414 (t) cc_final: 0.8109 (m) REVERT: D 202 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7422 (p0) REVERT: D 308 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7855 (mttp) REVERT: D 336 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7702 (ttt180) REVERT: D 344 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7249 (mt-10) REVERT: H 141 THR cc_start: 0.7897 (m) cc_final: 0.7594 (p) REVERT: H 154 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8163 (p) REVERT: H 180 ARG cc_start: 0.8412 (mtt180) cc_final: 0.8203 (mtt180) outliers start: 42 outliers final: 22 residues processed: 274 average time/residue: 1.0293 time to fit residues: 302.7959 Evaluate side-chains 267 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 241 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 67 SER 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 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER 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 336 ARG 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 154 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 233 LEU 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: 0.8980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3226 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= 0.275 Angle : 0.580 7.757 12484 Z= 0.303 Chirality : 0.043 0.160 1437 Planarity : 0.004 0.041 1576 Dihedral : 5.397 69.957 1262 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.01 % Allowed : 17.43 % Favored : 77.56 % 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: 0.73 (0.25), residues: 1150 helix: 1.72 (0.25), residues: 411 sheet: -0.28 (0.29), residues: 286 loop : -0.02 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.022 0.002 PHE A 55 TYR 0.017 0.002 TYR D 179 ARG 0.007 0.001 ARG A 38 *********************** 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 291 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 243 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8307 (p) cc_final: 0.7962 (p) REVERT: A 9 ASP cc_start: 0.7256 (m-30) cc_final: 0.6909 (m-30) REVERT: A 39 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6544 (mt-10) REVERT: A 201 PHE cc_start: 0.8323 (m-80) cc_final: 0.7712 (m-80) REVERT: A 202 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: A 276 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7211 (ttpp) REVERT: A 307 GLU cc_start: 0.7464 (tp30) cc_final: 0.7122 (tp30) REVERT: A 322 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7868 (ttmm) REVERT: A 326 SER cc_start: 0.8286 (p) cc_final: 0.8052 (t) REVERT: B 98 SER cc_start: 0.7843 (p) cc_final: 0.7499 (t) REVERT: B 191 SER cc_start: 0.7966 (p) cc_final: 0.7762 (p) REVERT: B 274 THR cc_start: 0.7764 (m) cc_final: 0.7466 (p) REVERT: D 74 THR cc_start: 0.7983 (t) cc_final: 0.7690 (p) REVERT: D 75 VAL cc_start: 0.8059 (p) cc_final: 0.7750 (t) REVERT: D 95 MET cc_start: 0.7503 (mtp) cc_final: 0.7248 (mtp) REVERT: D 323 PHE cc_start: 0.8321 (m-80) cc_final: 0.7975 (m-80) REVERT: D 329 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7973 (tt) REVERT: D 336 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7718 (ttt180) REVERT: H 20 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7642 (pp) REVERT: H 30 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8115 (t) REVERT: H 63 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8158 (t) outliers start: 48 outliers final: 20 residues processed: 265 average time/residue: 1.1182 time to fit residues: 317.2984 Evaluate side-chains 270 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 276 LYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER 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 219 LEU Chi-restraints excluded: chain D residue 329 ILE 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 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 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: 1.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9196 Z= 0.286 Angle : 0.583 9.895 12484 Z= 0.302 Chirality : 0.044 0.187 1437 Planarity : 0.004 0.042 1576 Dihedral : 5.346 69.903 1262 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.49 % Allowed : 18.89 % Favored : 76.62 % 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: 0.71 (0.25), residues: 1150 helix: 1.79 (0.25), residues: 409 sheet: -0.27 (0.29), residues: 287 loop : -0.13 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.027 0.002 PHE A 55 TYR 0.016 0.002 TYR D 179 ARG 0.007 0.001 ARG A 38 *********************** 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 283 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 240 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8324 (p) cc_final: 0.7993 (p) REVERT: A 9 ASP cc_start: 0.7256 (m-30) cc_final: 0.6910 (m-30) REVERT: A 39 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6663 (mt-10) REVERT: A 41 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7843 (mttm) REVERT: A 201 PHE cc_start: 0.8363 (m-80) cc_final: 0.7673 (m-80) REVERT: A 307 GLU cc_start: 0.7439 (tp30) cc_final: 0.7106 (tp30) REVERT: A 326 SER cc_start: 0.8272 (p) cc_final: 0.8049 (t) REVERT: B 98 SER cc_start: 0.7863 (p) cc_final: 0.7526 (t) REVERT: B 274 THR cc_start: 0.7699 (m) cc_final: 0.7414 (p) REVERT: B 312 ASP cc_start: 0.6883 (t0) cc_final: 0.6659 (t70) REVERT: D 74 THR cc_start: 0.7998 (t) cc_final: 0.7720 (p) REVERT: D 75 VAL cc_start: 0.8090 (p) cc_final: 0.7781 (t) REVERT: D 227 VAL cc_start: 0.8172 (t) cc_final: 0.7929 (m) REVERT: D 323 PHE cc_start: 0.8358 (m-80) cc_final: 0.7922 (m-80) REVERT: D 329 ILE cc_start: 0.8175 (tp) cc_final: 0.7965 (tt) REVERT: D 336 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7830 (ttt180) REVERT: H 20 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7685 (pp) REVERT: H 30 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8097 (t) REVERT: H 63 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8179 (t) REVERT: H 215 THR cc_start: 0.7986 (p) cc_final: 0.7732 (p) outliers start: 43 outliers final: 20 residues processed: 262 average time/residue: 1.0988 time to fit residues: 308.2389 Evaluate side-chains 265 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain B residue 97 SER 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 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 51 ILE 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 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR 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 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9196 Z= 0.302 Angle : 0.592 8.877 12484 Z= 0.306 Chirality : 0.044 0.155 1437 Planarity : 0.004 0.042 1576 Dihedral : 5.335 70.352 1262 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.86 % Allowed : 20.04 % Favored : 76.10 % 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: 0.65 (0.25), residues: 1150 helix: 1.82 (0.25), residues: 408 sheet: -0.39 (0.29), residues: 296 loop : -0.17 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.025 0.002 PHE A 55 TYR 0.016 0.002 TYR D 179 ARG 0.006 0.000 ARG A 38 *********************** 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 278 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 241 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8331 (p) cc_final: 0.8004 (p) REVERT: A 9 ASP cc_start: 0.7278 (m-30) cc_final: 0.6943 (m-30) REVERT: A 39 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6649 (mt-10) REVERT: A 41 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7853 (mttm) REVERT: A 201 PHE cc_start: 0.8374 (m-80) cc_final: 0.7647 (m-80) REVERT: A 307 GLU cc_start: 0.7411 (tp30) cc_final: 0.7090 (tp30) REVERT: A 326 SER cc_start: 0.8267 (p) cc_final: 0.8061 (t) REVERT: A 341 PHE cc_start: 0.8446 (t80) cc_final: 0.8044 (t80) REVERT: B 98 SER cc_start: 0.8005 (p) cc_final: 0.7719 (t) REVERT: B 312 ASP cc_start: 0.6911 (t0) cc_final: 0.6671 (t70) REVERT: D 75 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7847 (t) REVERT: D 200 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5892 (mp) REVERT: D 323 PHE cc_start: 0.8335 (m-80) cc_final: 0.7937 (m-80) REVERT: D 329 ILE cc_start: 0.8171 (tp) cc_final: 0.7961 (tt) REVERT: D 336 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7818 (ttt180) REVERT: H 63 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8186 (t) REVERT: H 215 THR cc_start: 0.7960 (p) cc_final: 0.7747 (p) outliers start: 37 outliers final: 22 residues processed: 258 average time/residue: 1.1350 time to fit residues: 313.4534 Evaluate side-chains 269 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER 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 200 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 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 155 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9196 Z= 0.230 Angle : 0.582 9.386 12484 Z= 0.297 Chirality : 0.043 0.187 1437 Planarity : 0.004 0.042 1576 Dihedral : 5.301 71.025 1262 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.28 % Allowed : 20.88 % Favored : 74.84 % 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: 0.70 (0.25), residues: 1150 helix: 1.87 (0.25), residues: 409 sheet: -0.33 (0.29), residues: 295 loop : -0.17 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS D 210 PHE 0.030 0.002 PHE A 55 TYR 0.016 0.002 TYR D 179 ARG 0.008 0.000 ARG A 38 *********************** 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 288 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8327 (p) cc_final: 0.8080 (p) REVERT: A 9 ASP cc_start: 0.7258 (m-30) cc_final: 0.6974 (m-30) REVERT: A 39 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 41 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7833 (mttm) REVERT: A 201 PHE cc_start: 0.8388 (m-80) cc_final: 0.7616 (m-80) REVERT: A 307 GLU cc_start: 0.7389 (tp30) cc_final: 0.7078 (tp30) REVERT: B 98 SER cc_start: 0.7977 (p) cc_final: 0.7637 (t) REVERT: B 227 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7770 (t) REVERT: B 312 ASP cc_start: 0.6883 (t0) cc_final: 0.6644 (t70) REVERT: D 75 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7844 (t) REVERT: D 323 PHE cc_start: 0.8323 (m-80) cc_final: 0.7953 (m-80) REVERT: D 329 ILE cc_start: 0.8154 (tp) cc_final: 0.7940 (tt) REVERT: D 336 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7773 (ttt180) REVERT: H 30 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8073 (t) REVERT: H 63 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8182 (t) REVERT: H 215 THR cc_start: 0.7948 (p) cc_final: 0.7732 (p) outliers start: 41 outliers final: 25 residues processed: 267 average time/residue: 1.1553 time to fit residues: 328.9167 Evaluate side-chains 270 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 SER 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 B residue 331 SER Chi-restraints excluded: chain B residue 334 SER 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 219 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 22 CYS 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 155 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3952 > 50: distance: 24 - 93: 11.846 distance: 27 - 90: 14.457 distance: 48 - 51: 3.416 distance: 51 - 52: 6.712 distance: 52 - 53: 5.528 distance: 53 - 54: 14.604 distance: 53 - 57: 15.142 distance: 55 - 56: 7.110 distance: 57 - 58: 6.742 distance: 57 - 177: 18.207 distance: 58 - 59: 13.427 distance: 58 - 61: 7.257 distance: 59 - 60: 17.732 distance: 59 - 64: 18.157 distance: 60 - 174: 34.762 distance: 61 - 62: 6.090 distance: 61 - 63: 9.337 distance: 64 - 65: 18.563 distance: 65 - 66: 19.032 distance: 65 - 68: 13.161 distance: 66 - 67: 8.493 distance: 66 - 70: 8.689 distance: 68 - 69: 10.825 distance: 70 - 71: 4.043 distance: 70 - 164: 14.224 distance: 71 - 72: 5.746 distance: 71 - 74: 5.719 distance: 72 - 73: 12.986 distance: 72 - 78: 7.104 distance: 73 - 161: 19.792 distance: 74 - 75: 9.403 distance: 74 - 76: 6.392 distance: 75 - 77: 4.985 distance: 78 - 79: 14.447 distance: 79 - 80: 24.084 distance: 79 - 82: 16.893 distance: 80 - 81: 17.479 distance: 80 - 84: 12.177 distance: 84 - 85: 9.349 distance: 84 - 148: 19.949 distance: 85 - 88: 4.385 distance: 86 - 87: 3.887 distance: 86 - 90: 3.766 distance: 87 - 145: 12.976 distance: 88 - 89: 17.777 distance: 89 - 201: 24.922 distance: 91 - 92: 5.326 distance: 91 - 94: 6.635 distance: 92 - 95: 3.259 distance: 95 - 96: 4.897 distance: 96 - 97: 12.598 distance: 96 - 99: 6.357 distance: 97 - 98: 10.889 distance: 97 - 101: 10.795 distance: 99 - 100: 8.605 distance: 101 - 102: 11.790 distance: 102 - 103: 11.665 distance: 102 - 105: 8.588 distance: 103 - 104: 13.993 distance: 103 - 107: 10.555 distance: 105 - 106: 3.090 distance: 108 - 109: 8.765 distance: 108 - 111: 4.936 distance: 109 - 110: 16.393 distance: 109 - 116: 8.278 distance: 111 - 112: 3.406 distance: 114 - 115: 3.455