Starting phenix.real_space_refine on Tue Feb 13 21:30:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/02_2024/8bmp_16120_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/02_2024/8bmp_16120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/02_2024/8bmp_16120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/02_2024/8bmp_16120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/02_2024/8bmp_16120_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/02_2024/8bmp_16120_updated.pdb" } resolution = 3.2 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= 0.009 sd= 0.103 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 5052 2.51 5 N 1283 2.21 5 O 1417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7794 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2130 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2183 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "C" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1321 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "D" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2101 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.58 Number of scatterers: 7794 At special positions: 0 Unit cell: (83.804, 85.848, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 5 15.00 Mg 1 11.99 O 1417 8.00 N 1283 7.00 C 5052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 7 sheets defined 54.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 102 through 113 removed outlier: 4.635A pdb=" N GLY A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.847A pdb=" N LYS A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 204 through 209 removed outlier: 4.289A pdb=" N GLY A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.665A pdb=" N SER A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.657A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 103 through 114 removed outlier: 4.244A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.694A pdb=" N PHE B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 178 through 194 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 248 through 259 Processing helix chain 'B' and resid 270 through 280 Processing helix chain 'C' and resid 13 through 31 removed outlier: 3.908A pdb=" N GLN C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 74 removed outlier: 3.850A pdb=" N TYR C 53 " --> pdb=" O MET C 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU C 54 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 55 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY C 56 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Proline residue: C 57 - end of helix removed outlier: 3.970A pdb=" N GLY C 60 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 67 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 100 Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 146 through 171 Proline residue: C 153 - end of helix removed outlier: 4.159A pdb=" N VAL C 158 " --> pdb=" O TRP C 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 18 No H-bonds generated for 'chain 'D' and resid 15 through 18' Processing helix chain 'D' and resid 21 through 37 removed outlier: 3.894A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 3.691A pdb=" N THR D 58 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 86 Proline residue: D 71 - end of helix removed outlier: 4.982A pdb=" N TRP D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N MET D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 128 Processing helix chain 'D' and resid 132 through 149 removed outlier: 3.764A pdb=" N THR D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix removed outlier: 4.846A pdb=" N LEU D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 184 Proline residue: D 168 - end of helix removed outlier: 3.820A pdb=" N ARG D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 225 removed outlier: 3.719A pdb=" N VAL D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Proline residue: D 202 - end of helix Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 244 through 262 Proline residue: D 248 - end of helix removed outlier: 3.810A pdb=" N CYS D 252 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 254 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET D 259 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.345A pdb=" N SER A 66 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.259A pdb=" N VAL A 164 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 166 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR A 196 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU A 167 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 40 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 212 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE A 39 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 214 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 223 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP A 217 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.717A pdb=" N PHE B 28 " --> pdb=" O PHE B 5 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.900A pdb=" N ALA B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS B 226 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 215 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 198 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 38 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLY B 40 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.511A pdb=" N TYR B 10 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR B 12 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE B 21 " --> pdb=" O TYR B 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 33 through 35 Processing sheet with id= G, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.598A pdb=" N LEU D 101 " --> pdb=" O TYR D 93 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 996 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: 2.13 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2456 1.34 - 1.46: 1683 1.46 - 1.58: 3747 1.58 - 1.70: 7 1.70 - 1.81: 68 Bond restraints: 7961 Sorted by residual: bond pdb=" C VAL D 167 " pdb=" N PRO D 168 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 1.97e+00 bond pdb=" C4 ADP B 301 " pdb=" C5 ADP B 301 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA SER A 27 " pdb=" C SER A 27 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.08e-02 8.57e+03 9.27e-01 bond pdb=" CA THR C 152 " pdb=" C THR C 152 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.26e-02 6.30e+03 7.83e-01 bond pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.74e-01 ... (remaining 7956 not shown) Histogram of bond angle deviations from ideal: 99.92 - 107.89: 332 107.89 - 115.87: 4908 115.87 - 123.85: 5360 123.85 - 131.83: 172 131.83 - 139.81: 25 Bond angle restraints: 10797 Sorted by residual: angle pdb=" N ILE D 98 " pdb=" CA ILE D 98 " pdb=" C ILE D 98 " ideal model delta sigma weight residual 113.71 110.15 3.56 9.50e-01 1.11e+00 1.40e+01 angle pdb=" N GLU B 6 " pdb=" CA GLU B 6 " pdb=" C GLU B 6 " ideal model delta sigma weight residual 109.94 104.74 5.20 1.57e+00 4.06e-01 1.10e+01 angle pdb=" C ASP A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta sigma weight residual 120.63 125.93 -5.30 1.61e+00 3.86e-01 1.08e+01 angle pdb=" N ASP A 268 " pdb=" CA ASP A 268 " pdb=" C ASP A 268 " ideal model delta sigma weight residual 112.34 116.45 -4.11 1.30e+00 5.92e-01 1.00e+01 angle pdb=" N GLY C 35 " pdb=" CA GLY C 35 " pdb=" C GLY C 35 " ideal model delta sigma weight residual 110.38 114.71 -4.33 1.42e+00 4.96e-01 9.30e+00 ... (remaining 10792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 4613 31.01 - 62.02: 123 62.02 - 93.03: 9 93.03 - 124.04: 0 124.04 - 155.04: 2 Dihedral angle restraints: 4747 sinusoidal: 1918 harmonic: 2829 Sorted by residual: dihedral pdb=" O2A ADP B 301 " pdb=" O3A ADP B 301 " pdb=" PA ADP B 301 " pdb=" PB ADP B 301 " ideal model delta sinusoidal sigma weight residual -60.00 95.05 -155.04 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O1B ADP B 301 " pdb=" O3A ADP B 301 " pdb=" PB ADP B 301 " pdb=" PA ADP B 301 " ideal model delta sinusoidal sigma weight residual -60.00 74.33 -134.34 1 2.00e+01 2.50e-03 4.08e+01 dihedral pdb=" CA ASP A 267 " pdb=" C ASP A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 692 0.029 - 0.057: 339 0.057 - 0.086: 127 0.086 - 0.114: 67 0.114 - 0.143: 18 Chirality restraints: 1243 Sorted by residual: chirality pdb=" CA THR C 152 " pdb=" N THR C 152 " pdb=" C THR C 152 " pdb=" CB THR C 152 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE C 123 " pdb=" N ILE C 123 " pdb=" C ILE C 123 " pdb=" CB ILE C 123 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1240 not shown) Planarity restraints: 1341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 270 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 271 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 271 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 271 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 93 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 252 " 0.007 2.00e-02 2.50e+03 1.08e-02 2.03e+00 pdb=" CG PHE B 252 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 252 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 252 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 252 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 252 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 252 " 0.001 2.00e-02 2.50e+03 ... (remaining 1338 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1585 2.78 - 3.31: 7664 3.31 - 3.84: 12680 3.84 - 4.37: 15237 4.37 - 4.90: 26079 Nonbonded interactions: 63245 Sorted by model distance: nonbonded pdb=" O GLU D 104 " pdb=" ND2 ASN D 108 " model vdw 2.246 2.520 nonbonded pdb=" OD2 ASP A 61 " pdb=" NZ LYS A 64 " model vdw 2.297 2.520 nonbonded pdb=" OG1 THR A 101 " pdb=" OD1 ASP A 104 " model vdw 2.327 2.440 nonbonded pdb=" OD2 ASP D 172 " pdb=" NZ LYS D 176 " model vdw 2.351 2.520 nonbonded pdb=" OD1 ASP A 266 " pdb=" N ASP A 267 " model vdw 2.378 2.520 ... (remaining 63240 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.580 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.570 Find NCS groups from input model: 0.260 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.003 0.035 7961 Z= 0.218 Angle : 0.636 7.246 10797 Z= 0.351 Chirality : 0.043 0.143 1243 Planarity : 0.004 0.050 1341 Dihedral : 14.233 155.045 2925 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.27), residues: 979 helix: 1.09 (0.22), residues: 571 sheet: 0.87 (0.71), residues: 62 loop : -0.65 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 276 HIS 0.007 0.001 HIS A 41 PHE 0.024 0.001 PHE B 252 TYR 0.012 0.001 TYR D 44 ARG 0.007 0.001 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.871 Fit side-chains REVERT: A 184 ASP cc_start: 0.7837 (m-30) cc_final: 0.7391 (m-30) REVERT: C 129 TRP cc_start: 0.8101 (m-10) cc_final: 0.7843 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2160 time to fit residues: 30.6300 Evaluate side-chains 96 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7961 Z= 0.304 Angle : 0.577 7.442 10797 Z= 0.286 Chirality : 0.044 0.150 1243 Planarity : 0.004 0.039 1341 Dihedral : 9.391 162.211 1091 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.60 % Allowed : 5.85 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 979 helix: 1.17 (0.22), residues: 573 sheet: 0.34 (0.69), residues: 62 loop : -0.51 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.002 0.001 HIS B 52 PHE 0.017 0.002 PHE B 252 TYR 0.012 0.002 TYR D 44 ARG 0.003 0.000 ARG D 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.863 Fit side-chains REVERT: A 184 ASP cc_start: 0.7878 (m-30) cc_final: 0.7421 (m-30) REVERT: C 129 TRP cc_start: 0.8133 (m-10) cc_final: 0.7796 (m-10) REVERT: D 203 MET cc_start: 0.8587 (ttm) cc_final: 0.8269 (ttm) outliers start: 5 outliers final: 2 residues processed: 104 average time/residue: 0.2462 time to fit residues: 35.0957 Evaluate side-chains 101 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.0170 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7961 Z= 0.171 Angle : 0.510 6.677 10797 Z= 0.251 Chirality : 0.041 0.140 1243 Planarity : 0.003 0.039 1341 Dihedral : 8.990 161.592 1091 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.84 % Allowed : 7.77 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 979 helix: 1.46 (0.22), residues: 563 sheet: 0.22 (0.68), residues: 62 loop : -0.56 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.002 0.000 HIS B 242 PHE 0.010 0.001 PHE B 252 TYR 0.008 0.001 TYR D 44 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.788 Fit side-chains REVERT: A 184 ASP cc_start: 0.7882 (m-30) cc_final: 0.7426 (m-30) REVERT: A 266 ASP cc_start: 0.7079 (t0) cc_final: 0.6809 (t0) outliers start: 7 outliers final: 2 residues processed: 106 average time/residue: 0.2165 time to fit residues: 30.6356 Evaluate side-chains 101 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7961 Z= 0.300 Angle : 0.567 6.964 10797 Z= 0.280 Chirality : 0.044 0.146 1243 Planarity : 0.004 0.039 1341 Dihedral : 8.952 158.819 1091 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.84 % Allowed : 9.56 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 979 helix: 1.24 (0.22), residues: 568 sheet: -0.15 (0.68), residues: 63 loop : -0.58 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 129 HIS 0.002 0.001 HIS B 52 PHE 0.010 0.001 PHE B 28 TYR 0.011 0.001 TYR B 162 ARG 0.006 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 0.906 Fit side-chains REVERT: A 184 ASP cc_start: 0.7872 (m-30) cc_final: 0.7417 (m-30) REVERT: A 266 ASP cc_start: 0.7218 (t0) cc_final: 0.6906 (t0) outliers start: 7 outliers final: 2 residues processed: 113 average time/residue: 0.2246 time to fit residues: 34.0467 Evaluate side-chains 104 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.0070 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7961 Z= 0.163 Angle : 0.514 6.244 10797 Z= 0.251 Chirality : 0.041 0.138 1243 Planarity : 0.003 0.039 1341 Dihedral : 8.628 153.236 1091 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.08 % Allowed : 10.87 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 979 helix: 1.62 (0.22), residues: 555 sheet: 0.11 (0.66), residues: 67 loop : -0.55 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 129 HIS 0.002 0.000 HIS B 242 PHE 0.008 0.001 PHE B 252 TYR 0.013 0.001 TYR A 248 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.887 Fit side-chains REVERT: A 184 ASP cc_start: 0.7884 (m-30) cc_final: 0.7437 (m-30) REVERT: A 266 ASP cc_start: 0.7394 (t0) cc_final: 0.7045 (t0) outliers start: 9 outliers final: 0 residues processed: 112 average time/residue: 0.2358 time to fit residues: 35.3786 Evaluate side-chains 100 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.1540 ------------------------------------------------------------------------------- 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: 0.8147 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7961 Z= 0.241 Angle : 0.547 6.353 10797 Z= 0.266 Chirality : 0.042 0.141 1243 Planarity : 0.003 0.040 1341 Dihedral : 8.577 148.235 1091 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 12.07 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 979 helix: 1.51 (0.22), residues: 554 sheet: 0.13 (0.64), residues: 72 loop : -0.57 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 129 HIS 0.002 0.000 HIS B 52 PHE 0.008 0.001 PHE A 8 TYR 0.010 0.001 TYR B 162 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.884 Fit side-chains REVERT: A 184 ASP cc_start: 0.7879 (m-30) cc_final: 0.7429 (m-30) REVERT: A 266 ASP cc_start: 0.7317 (t0) cc_final: 0.7090 (t0) REVERT: D 203 MET cc_start: 0.8812 (ttp) cc_final: 0.8489 (ttm) outliers start: 7 outliers final: 2 residues processed: 110 average time/residue: 0.2111 time to fit residues: 31.1786 Evaluate side-chains 104 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain D residue 130 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.0010 chunk 37 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7961 Z= 0.155 Angle : 0.512 6.432 10797 Z= 0.249 Chirality : 0.041 0.135 1243 Planarity : 0.003 0.039 1341 Dihedral : 8.274 140.046 1091 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.60 % Allowed : 12.66 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 979 helix: 1.69 (0.22), residues: 557 sheet: 0.20 (0.65), residues: 72 loop : -0.51 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 129 HIS 0.001 0.000 HIS B 242 PHE 0.018 0.001 PHE B 252 TYR 0.007 0.001 TYR C 134 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.834 Fit side-chains REVERT: A 184 ASP cc_start: 0.7886 (m-30) cc_final: 0.7433 (m-30) REVERT: A 266 ASP cc_start: 0.7190 (t0) cc_final: 0.6337 (m-30) REVERT: B 135 LYS cc_start: 0.8446 (pttt) cc_final: 0.8164 (pttt) REVERT: D 44 TYR cc_start: 0.7837 (m-80) cc_final: 0.7339 (m-80) REVERT: D 203 MET cc_start: 0.8722 (ttp) cc_final: 0.8510 (ttp) outliers start: 5 outliers final: 2 residues processed: 108 average time/residue: 0.2145 time to fit residues: 31.2537 Evaluate side-chains 104 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain D residue 130 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7961 Z= 0.223 Angle : 0.544 7.669 10797 Z= 0.263 Chirality : 0.042 0.139 1243 Planarity : 0.003 0.039 1341 Dihedral : 8.233 134.779 1091 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.08 % Allowed : 12.19 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 979 helix: 1.59 (0.22), residues: 555 sheet: 0.14 (0.65), residues: 72 loop : -0.56 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 129 HIS 0.001 0.000 HIS B 242 PHE 0.009 0.001 PHE A 8 TYR 0.014 0.001 TYR A 248 ARG 0.007 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.926 Fit side-chains REVERT: A 184 ASP cc_start: 0.7882 (m-30) cc_final: 0.7431 (m-30) REVERT: A 266 ASP cc_start: 0.7203 (t0) cc_final: 0.6322 (m-30) REVERT: B 135 LYS cc_start: 0.8481 (pttt) cc_final: 0.8228 (pttm) REVERT: D 203 MET cc_start: 0.8753 (ttp) cc_final: 0.8434 (ttm) outliers start: 9 outliers final: 4 residues processed: 108 average time/residue: 0.2107 time to fit residues: 30.8232 Evaluate side-chains 106 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 130 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.8140 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7961 Z= 0.234 Angle : 0.553 7.844 10797 Z= 0.268 Chirality : 0.043 0.141 1243 Planarity : 0.003 0.039 1341 Dihedral : 8.182 127.950 1091 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.08 % Allowed : 12.43 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 979 helix: 1.55 (0.22), residues: 554 sheet: 0.09 (0.65), residues: 72 loop : -0.60 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 276 HIS 0.001 0.000 HIS B 52 PHE 0.011 0.001 PHE A 246 TYR 0.009 0.001 TYR B 10 ARG 0.006 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.903 Fit side-chains REVERT: A 184 ASP cc_start: 0.7856 (m-30) cc_final: 0.7408 (m-30) REVERT: A 266 ASP cc_start: 0.7186 (t0) cc_final: 0.6340 (m-30) REVERT: A 276 TRP cc_start: 0.8814 (t-100) cc_final: 0.8536 (t-100) REVERT: B 135 LYS cc_start: 0.8531 (pttt) cc_final: 0.8067 (ptpt) REVERT: D 203 MET cc_start: 0.8765 (ttp) cc_final: 0.8468 (ttm) outliers start: 9 outliers final: 6 residues processed: 105 average time/residue: 0.2166 time to fit residues: 30.5135 Evaluate side-chains 106 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7961 Z= 0.162 Angle : 0.522 7.453 10797 Z= 0.251 Chirality : 0.041 0.134 1243 Planarity : 0.003 0.039 1341 Dihedral : 7.825 120.283 1091 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.19 % Allowed : 12.19 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 979 helix: 1.72 (0.22), residues: 558 sheet: 0.12 (0.65), residues: 72 loop : -0.55 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 276 HIS 0.001 0.000 HIS B 242 PHE 0.009 0.001 PHE A 246 TYR 0.013 0.001 TYR A 248 ARG 0.006 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.669 Fit side-chains REVERT: A 184 ASP cc_start: 0.7811 (m-30) cc_final: 0.7356 (m-30) REVERT: A 266 ASP cc_start: 0.7113 (t0) cc_final: 0.6304 (m-30) REVERT: A 276 TRP cc_start: 0.8796 (t-100) cc_final: 0.8540 (t-100) REVERT: B 135 LYS cc_start: 0.8469 (pttt) cc_final: 0.8051 (ptpt) REVERT: D 203 MET cc_start: 0.8703 (ttp) cc_final: 0.8432 (ttm) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.2055 time to fit residues: 30.8496 Evaluate side-chains 105 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107018 restraints weight = 10221.239| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.12 r_work: 0.3107 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7961 Z= 0.252 Angle : 0.564 8.953 10797 Z= 0.271 Chirality : 0.043 0.141 1243 Planarity : 0.003 0.039 1341 Dihedral : 7.894 116.517 1091 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.84 % Allowed : 13.26 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 979 helix: 1.53 (0.22), residues: 554 sheet: 0.02 (0.65), residues: 72 loop : -0.62 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 276 HIS 0.002 0.001 HIS B 52 PHE 0.010 0.001 PHE D 149 TYR 0.009 0.001 TYR B 162 ARG 0.005 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.60 seconds wall clock time: 34 minutes 45.65 seconds (2085.65 seconds total)