Starting phenix.real_space_refine on Wed Feb 12 01:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r0c_14221/02_2025/7r0c_14221.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r0c_14221/02_2025/7r0c_14221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r0c_14221/02_2025/7r0c_14221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r0c_14221/02_2025/7r0c_14221.map" model { file = "/net/cci-nas-00/data/ceres_data/7r0c_14221/02_2025/7r0c_14221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r0c_14221/02_2025/7r0c_14221.cif" } resolution = 4.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 39 5.16 5 C 4365 2.51 5 N 1158 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6816 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2181 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2810 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1750 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 4.42, per 1000 atoms: 0.65 Number of scatterers: 6816 At special positions: 0 Unit cell: (83.2, 99.84, 139.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 6 15.00 O 1248 8.00 N 1158 7.00 C 4365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 6 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 929.0 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 11 sheets defined 29.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 33 through 69 Processing helix chain 'A' and resid 72 through 103 removed outlier: 3.924A pdb=" N ILE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 109 through 140 removed outlier: 4.001A pdb=" N ARG A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.582A pdb=" N PHE A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 228 removed outlier: 5.019A pdb=" N ALA A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix removed outlier: 3.938A pdb=" N ILE A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.583A pdb=" N VAL A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 5.570A pdb=" N SER A 315 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.574A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.663A pdb=" N ASN C 280 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 282 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.529A pdb=" N PHE D 86 " --> pdb=" O PRO D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 157 Processing helix chain 'D' and resid 188 through 191 Processing helix chain 'D' and resid 213 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363 Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.102A pdb=" N PHE C 27 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL C 53 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE C 61 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP C 78 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188 Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 208 removed outlier: 4.128A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 318 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 239 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER C 320 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLN C 237 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS C 322 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL C 235 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS C 324 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 233 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS C 326 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 231 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 328 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 231 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU C 257 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 233 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET C 255 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 235 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 237 " --> pdb=" O CYS C 251 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS C 251 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 239 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 7 through 9 Processing sheet with id=AA8, first strand: chain 'D' and resid 56 through 57 removed outlier: 6.413A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR D 52 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 36 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 129 through 133 Processing sheet with id=AB1, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.376A pdb=" N GLY D 136 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE D 160 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER D 176 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP D 162 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 172 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.376A pdb=" N GLY D 136 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR D 235 " --> pdb=" O ARG D 224 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 828 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: 1.95 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1179 1.32 - 1.45: 1796 1.45 - 1.57: 3926 1.57 - 1.69: 22 1.69 - 1.81: 52 Bond restraints: 6975 Sorted by residual: bond pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.717 1.620 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O1P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O1P TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O3P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 6970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 9271 2.56 - 5.11: 193 5.11 - 7.67: 27 7.67 - 10.23: 6 10.23 - 12.78: 1 Bond angle restraints: 9498 Sorted by residual: angle pdb=" N ILE A 74 " pdb=" CA ILE A 74 " pdb=" C ILE A 74 " ideal model delta sigma weight residual 110.42 101.79 8.63 9.60e-01 1.09e+00 8.08e+01 angle pdb=" N VAL A 76 " pdb=" CA VAL A 76 " pdb=" C VAL A 76 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.93e+01 angle pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 113.84 107.29 6.55 1.30e+00 5.92e-01 2.53e+01 angle pdb=" CA LYS D 202 " pdb=" CB LYS D 202 " pdb=" CG LYS D 202 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C LEU C 68 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " ideal model delta sigma weight residual 122.61 129.40 -6.79 1.56e+00 4.11e-01 1.89e+01 ... (remaining 9493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 3812 16.88 - 33.77: 308 33.77 - 50.65: 54 50.65 - 67.54: 9 67.54 - 84.42: 8 Dihedral angle restraints: 4191 sinusoidal: 1628 harmonic: 2563 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -141.74 55.74 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS B 1 " pdb=" SG CYS B 1 " pdb=" SG CYS B 6 " pdb=" CB CYS B 6 " ideal model delta sinusoidal sigma weight residual 93.00 45.16 47.84 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA ARG D 226 " pdb=" C ARG D 226 " pdb=" N GLN D 227 " pdb=" CA GLN D 227 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 4188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1040 0.108 - 0.215: 43 0.215 - 0.323: 1 0.323 - 0.430: 1 0.430 - 0.538: 1 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.97 -0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CA TRP A 71 " pdb=" N TRP A 71 " pdb=" C TRP A 71 " pdb=" CB TRP A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1083 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.015 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP A 99 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 94 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 95 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 359 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO C 360 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 180 2.66 - 3.22: 7059 3.22 - 3.78: 11171 3.78 - 4.34: 14375 4.34 - 4.90: 22454 Nonbonded interactions: 55239 Sorted by model distance: nonbonded pdb=" O ASN C 222 " pdb=" N SER C 265 " model vdw 2.100 3.120 nonbonded pdb=" OE1 GLN D 9 " pdb=" OG1 THR D 105 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR C 56 " pdb=" O ALA C 82 " model vdw 2.190 3.040 nonbonded pdb=" NZ LYS C 11 " pdb=" O ARG C 165 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP C 204 " pdb=" OH TYR C 208 " model vdw 2.210 3.040 ... (remaining 55234 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.620 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 6975 Z= 0.322 Angle : 0.909 12.782 9498 Z= 0.523 Chirality : 0.052 0.538 1086 Planarity : 0.005 0.060 1191 Dihedral : 13.187 84.422 2516 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.32 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 846 helix: -0.59 (0.32), residues: 209 sheet: -0.36 (0.34), residues: 245 loop : -0.59 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 99 HIS 0.006 0.002 HIS C 159 PHE 0.023 0.002 PHE D 228 TYR 0.020 0.002 TYR A 128 ARG 0.008 0.001 ARG D 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9158 (ppp) cc_final: 0.8925 (ppp) REVERT: A 288 PHE cc_start: 0.8903 (m-80) cc_final: 0.8337 (m-80) REVERT: C 75 PHE cc_start: 0.6481 (m-80) cc_final: 0.5776 (m-10) REVERT: C 129 LEU cc_start: 0.9301 (mt) cc_final: 0.9092 (mt) REVERT: D 48 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8827 (tmtt) REVERT: D 49 LEU cc_start: 0.8528 (tp) cc_final: 0.8280 (tp) REVERT: D 50 LEU cc_start: 0.8422 (mt) cc_final: 0.7655 (mt) REVERT: D 74 PHE cc_start: 0.9063 (m-80) cc_final: 0.8473 (m-80) REVERT: D 195 THR cc_start: 0.8680 (m) cc_final: 0.8416 (p) REVERT: D 209 MET cc_start: 0.6815 (mpp) cc_final: 0.6419 (mpp) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2022 time to fit residues: 34.8211 Evaluate side-chains 95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN C 122 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 281 ASN D 9 GLN D 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.113142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091417 restraints weight = 27321.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094533 restraints weight = 17226.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096692 restraints weight = 12328.911| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6975 Z= 0.189 Angle : 0.646 7.106 9498 Z= 0.329 Chirality : 0.044 0.174 1086 Planarity : 0.005 0.057 1191 Dihedral : 6.228 72.584 965 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.29), residues: 846 helix: -0.01 (0.33), residues: 211 sheet: -0.18 (0.34), residues: 244 loop : -0.68 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 99 HIS 0.005 0.001 HIS A 75 PHE 0.022 0.001 PHE D 228 TYR 0.013 0.001 TYR A 128 ARG 0.002 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9096 (ppp) cc_final: 0.8793 (ppp) REVERT: A 272 MET cc_start: 0.8509 (ppp) cc_final: 0.8259 (ppp) REVERT: A 288 PHE cc_start: 0.8932 (m-80) cc_final: 0.8434 (m-80) REVERT: C 10 LYS cc_start: 0.7668 (pttt) cc_final: 0.7116 (pttt) REVERT: C 75 PHE cc_start: 0.6400 (m-80) cc_final: 0.5631 (m-10) REVERT: C 172 GLN cc_start: 0.8742 (mp-120) cc_final: 0.8066 (mp-120) REVERT: C 315 LEU cc_start: 0.9207 (mm) cc_final: 0.9004 (mm) REVERT: D 48 LYS cc_start: 0.8788 (tmtt) cc_final: 0.8574 (tptt) REVERT: D 49 LEU cc_start: 0.8449 (tp) cc_final: 0.8028 (tp) REVERT: D 50 LEU cc_start: 0.8843 (mt) cc_final: 0.8363 (mt) REVERT: D 74 PHE cc_start: 0.9083 (m-80) cc_final: 0.8465 (m-80) REVERT: D 75 THR cc_start: 0.8612 (p) cc_final: 0.8306 (p) REVERT: D 195 THR cc_start: 0.8834 (m) cc_final: 0.8602 (p) REVERT: D 209 MET cc_start: 0.6928 (mpp) cc_final: 0.6383 (mpp) REVERT: D 234 ASP cc_start: 0.8617 (p0) cc_final: 0.8285 (p0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1924 time to fit residues: 33.5722 Evaluate side-chains 97 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.114404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092226 restraints weight = 27633.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.095419 restraints weight = 17187.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.097559 restraints weight = 12214.696| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6975 Z= 0.168 Angle : 0.617 6.471 9498 Z= 0.313 Chirality : 0.044 0.173 1086 Planarity : 0.005 0.057 1191 Dihedral : 6.057 72.715 965 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.43 (0.29), residues: 846 helix: 0.25 (0.34), residues: 211 sheet: -0.02 (0.35), residues: 247 loop : -0.66 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 99 HIS 0.005 0.001 HIS C 159 PHE 0.020 0.001 PHE D 228 TYR 0.022 0.001 TYR D 52 ARG 0.004 0.000 ARG D 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9760 (mm) cc_final: 0.9559 (mm) REVERT: A 133 MET cc_start: 0.9108 (ppp) cc_final: 0.8834 (ppp) REVERT: A 134 THR cc_start: 0.9088 (p) cc_final: 0.8876 (p) REVERT: A 272 MET cc_start: 0.8660 (ppp) cc_final: 0.8423 (ppp) REVERT: A 288 PHE cc_start: 0.8813 (m-80) cc_final: 0.8599 (m-80) REVERT: C 29 ASP cc_start: 0.8044 (t0) cc_final: 0.7591 (t0) REVERT: C 161 ARG cc_start: 0.8222 (tpt90) cc_final: 0.7913 (tpt90) REVERT: C 172 GLN cc_start: 0.8688 (mp-120) cc_final: 0.7826 (mp-120) REVERT: C 315 LEU cc_start: 0.9107 (mm) cc_final: 0.8859 (mm) REVERT: D 74 PHE cc_start: 0.9062 (m-80) cc_final: 0.8740 (m-80) REVERT: D 193 ARG cc_start: 0.8013 (ttt180) cc_final: 0.7651 (ttt180) REVERT: D 195 THR cc_start: 0.8729 (m) cc_final: 0.8413 (p) REVERT: D 207 LEU cc_start: 0.9091 (tp) cc_final: 0.8769 (tp) REVERT: D 209 MET cc_start: 0.7302 (mpp) cc_final: 0.5909 (mpp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2040 time to fit residues: 34.4656 Evaluate side-chains 99 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 0.0270 chunk 65 optimal weight: 7.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.112332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.090406 restraints weight = 28787.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093480 restraints weight = 18028.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.095629 restraints weight = 12842.074| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6975 Z= 0.197 Angle : 0.624 6.735 9498 Z= 0.317 Chirality : 0.044 0.157 1086 Planarity : 0.005 0.057 1191 Dihedral : 6.002 74.981 965 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.33 (0.29), residues: 846 helix: 0.47 (0.35), residues: 208 sheet: -0.24 (0.34), residues: 265 loop : -0.46 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 173 HIS 0.004 0.001 HIS C 159 PHE 0.020 0.001 PHE A 166 TYR 0.011 0.001 TYR A 280 ARG 0.002 0.000 ARG C 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7411 (mmp) cc_final: 0.7184 (mmp) REVERT: A 130 ILE cc_start: 0.9733 (mm) cc_final: 0.9496 (mm) REVERT: A 133 MET cc_start: 0.9242 (ppp) cc_final: 0.9023 (ppp) REVERT: A 288 PHE cc_start: 0.8809 (m-80) cc_final: 0.8482 (m-80) REVERT: C 29 ASP cc_start: 0.8232 (t0) cc_final: 0.7503 (t0) REVERT: C 223 ASN cc_start: 0.8080 (m-40) cc_final: 0.7735 (p0) REVERT: D 65 PHE cc_start: 0.7934 (m-80) cc_final: 0.7651 (m-80) REVERT: D 74 PHE cc_start: 0.9089 (m-80) cc_final: 0.8814 (m-80) REVERT: D 193 ARG cc_start: 0.8095 (ttt180) cc_final: 0.7815 (ttt180) REVERT: D 195 THR cc_start: 0.8764 (m) cc_final: 0.8517 (p) REVERT: D 209 MET cc_start: 0.7359 (mpp) cc_final: 0.6826 (mmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2015 time to fit residues: 32.9963 Evaluate side-chains 98 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.111305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089654 restraints weight = 28610.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092653 restraints weight = 18024.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.094680 restraints weight = 12928.736| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6975 Z= 0.216 Angle : 0.637 6.930 9498 Z= 0.323 Chirality : 0.044 0.145 1086 Planarity : 0.005 0.057 1191 Dihedral : 6.107 77.805 965 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.34 (0.29), residues: 846 helix: 0.44 (0.34), residues: 208 sheet: -0.14 (0.34), residues: 250 loop : -0.52 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 99 HIS 0.004 0.001 HIS C 159 PHE 0.018 0.002 PHE D 228 TYR 0.027 0.002 TYR D 52 ARG 0.005 0.001 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7521 (mmp) cc_final: 0.7282 (mmp) REVERT: A 133 MET cc_start: 0.9181 (ppp) cc_final: 0.8833 (ppp) REVERT: A 134 THR cc_start: 0.9292 (p) cc_final: 0.9080 (p) REVERT: A 272 MET cc_start: 0.8311 (ppp) cc_final: 0.8038 (ppp) REVERT: A 288 PHE cc_start: 0.8855 (m-80) cc_final: 0.8543 (m-80) REVERT: C 29 ASP cc_start: 0.8201 (t0) cc_final: 0.7746 (t0) REVERT: C 172 GLN cc_start: 0.8581 (mp-120) cc_final: 0.7686 (mp-120) REVERT: C 223 ASN cc_start: 0.8100 (m-40) cc_final: 0.7827 (p0) REVERT: D 57 LEU cc_start: 0.8731 (pp) cc_final: 0.8397 (pp) REVERT: D 193 ARG cc_start: 0.8149 (ttt180) cc_final: 0.7696 (ttt-90) REVERT: D 195 THR cc_start: 0.8780 (m) cc_final: 0.8538 (p) REVERT: D 209 MET cc_start: 0.7379 (mpp) cc_final: 0.6828 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1913 time to fit residues: 31.5830 Evaluate side-chains 97 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 0.0170 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.108167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086508 restraints weight = 29704.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089422 restraints weight = 18482.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.091492 restraints weight = 13245.791| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6975 Z= 0.292 Angle : 0.701 7.653 9498 Z= 0.361 Chirality : 0.046 0.153 1086 Planarity : 0.006 0.073 1191 Dihedral : 6.459 79.709 965 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.46 (0.30), residues: 846 helix: 0.34 (0.35), residues: 202 sheet: -0.46 (0.34), residues: 251 loop : -0.40 (0.34), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 284 HIS 0.005 0.002 HIS A 80 PHE 0.025 0.002 PHE C 27 TYR 0.016 0.002 TYR A 325 ARG 0.007 0.001 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7625 (mmp) cc_final: 0.7370 (mmp) REVERT: A 133 MET cc_start: 0.8988 (ppp) cc_final: 0.8667 (ppp) REVERT: A 134 THR cc_start: 0.9396 (p) cc_final: 0.9178 (p) REVERT: A 288 PHE cc_start: 0.8931 (m-80) cc_final: 0.8712 (m-80) REVERT: C 172 GLN cc_start: 0.8438 (mp-120) cc_final: 0.7775 (mp-120) REVERT: D 49 LEU cc_start: 0.8606 (tp) cc_final: 0.8301 (tp) REVERT: D 50 LEU cc_start: 0.8486 (mm) cc_final: 0.7313 (mm) REVERT: D 193 ARG cc_start: 0.8185 (ttt180) cc_final: 0.7760 (ttt-90) REVERT: D 195 THR cc_start: 0.8821 (m) cc_final: 0.8592 (p) REVERT: D 209 MET cc_start: 0.7018 (mpp) cc_final: 0.6168 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1891 time to fit residues: 30.0238 Evaluate side-chains 95 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 67 optimal weight: 0.0870 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.112837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.090777 restraints weight = 27783.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093849 restraints weight = 17150.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.095955 restraints weight = 12156.579| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6975 Z= 0.173 Angle : 0.644 6.954 9498 Z= 0.321 Chirality : 0.045 0.157 1086 Planarity : 0.005 0.072 1191 Dihedral : 6.070 77.668 965 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.27 (0.30), residues: 846 helix: 0.61 (0.36), residues: 202 sheet: -0.23 (0.34), residues: 250 loop : -0.44 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 284 HIS 0.004 0.001 HIS A 80 PHE 0.022 0.002 PHE A 166 TYR 0.027 0.002 TYR D 52 ARG 0.004 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9056 (ppp) cc_final: 0.8791 (ppp) REVERT: A 272 MET cc_start: 0.8395 (ppp) cc_final: 0.8190 (ppp) REVERT: C 29 ASP cc_start: 0.7951 (t0) cc_final: 0.7556 (t0) REVERT: C 129 LEU cc_start: 0.9187 (mt) cc_final: 0.8975 (mt) REVERT: C 172 GLN cc_start: 0.8630 (mp-120) cc_final: 0.7928 (mp-120) REVERT: C 315 LEU cc_start: 0.9116 (mm) cc_final: 0.8907 (mm) REVERT: D 48 LYS cc_start: 0.8306 (tmtt) cc_final: 0.8087 (tptt) REVERT: D 57 LEU cc_start: 0.8871 (pp) cc_final: 0.8574 (pp) REVERT: D 90 TYR cc_start: 0.8094 (m-10) cc_final: 0.7218 (m-80) REVERT: D 193 ARG cc_start: 0.8207 (ttt180) cc_final: 0.7984 (ttt180) REVERT: D 195 THR cc_start: 0.8757 (m) cc_final: 0.8555 (p) REVERT: D 209 MET cc_start: 0.6908 (mpp) cc_final: 0.6431 (mmm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1904 time to fit residues: 32.3163 Evaluate side-chains 100 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085681 restraints weight = 29715.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088445 restraints weight = 18933.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090402 restraints weight = 13735.702| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6975 Z= 0.347 Angle : 0.748 8.007 9498 Z= 0.387 Chirality : 0.048 0.161 1086 Planarity : 0.006 0.069 1191 Dihedral : 6.600 80.053 965 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 846 helix: 0.24 (0.35), residues: 202 sheet: -0.44 (0.35), residues: 235 loop : -0.51 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP A 99 HIS 0.006 0.002 HIS C 30 PHE 0.026 0.003 PHE C 27 TYR 0.017 0.002 TYR D 181 ARG 0.016 0.001 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 THR cc_start: 0.9579 (m) cc_final: 0.9196 (m) REVERT: A 272 MET cc_start: 0.8569 (ppp) cc_final: 0.8343 (ppp) REVERT: A 280 TYR cc_start: 0.8914 (t80) cc_final: 0.8665 (t80) REVERT: A 284 TRP cc_start: 0.8578 (m-10) cc_final: 0.8011 (m-10) REVERT: C 172 GLN cc_start: 0.8501 (mp-120) cc_final: 0.7920 (mp-120) REVERT: D 65 PHE cc_start: 0.7488 (m-80) cc_final: 0.7233 (m-80) REVERT: D 90 TYR cc_start: 0.8085 (m-10) cc_final: 0.7483 (m-80) REVERT: D 193 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7742 (ttt180) REVERT: D 195 THR cc_start: 0.8909 (m) cc_final: 0.8703 (p) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1837 time to fit residues: 27.7501 Evaluate side-chains 91 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089528 restraints weight = 28813.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.092511 restraints weight = 18103.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094563 restraints weight = 12945.963| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6975 Z= 0.205 Angle : 0.674 6.895 9498 Z= 0.339 Chirality : 0.046 0.172 1086 Planarity : 0.005 0.059 1191 Dihedral : 6.321 79.200 965 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.44 (0.30), residues: 846 helix: 0.34 (0.35), residues: 203 sheet: -0.28 (0.35), residues: 235 loop : -0.52 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 99 HIS 0.005 0.001 HIS A 80 PHE 0.019 0.002 PHE A 287 TYR 0.025 0.002 TYR D 52 ARG 0.008 0.001 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8936 (ppp) cc_final: 0.8686 (ppp) REVERT: A 134 THR cc_start: 0.9519 (m) cc_final: 0.9191 (m) REVERT: A 212 MET cc_start: 0.8893 (ppp) cc_final: 0.8685 (ppp) REVERT: A 272 MET cc_start: 0.8603 (ppp) cc_final: 0.8346 (ppp) REVERT: C 29 ASP cc_start: 0.8106 (t0) cc_final: 0.7710 (t0) REVERT: C 129 LEU cc_start: 0.9156 (mt) cc_final: 0.8906 (mt) REVERT: C 172 GLN cc_start: 0.8609 (mp-120) cc_final: 0.7998 (mp-120) REVERT: C 315 LEU cc_start: 0.9141 (mm) cc_final: 0.8918 (mm) REVERT: D 65 PHE cc_start: 0.7499 (m-80) cc_final: 0.7242 (m-80) REVERT: D 90 TYR cc_start: 0.7843 (m-10) cc_final: 0.7236 (m-80) REVERT: D 193 ARG cc_start: 0.8178 (ttt180) cc_final: 0.7976 (ttt180) REVERT: D 195 THR cc_start: 0.8832 (m) cc_final: 0.8631 (p) REVERT: D 209 MET cc_start: 0.6951 (mpp) cc_final: 0.6469 (mmm) REVERT: D 226 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8223 (ttp80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1993 time to fit residues: 34.1135 Evaluate side-chains 98 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.088186 restraints weight = 29272.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091269 restraints weight = 18033.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093409 restraints weight = 12770.546| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6975 Z= 0.234 Angle : 0.684 6.897 9498 Z= 0.349 Chirality : 0.046 0.156 1086 Planarity : 0.005 0.060 1191 Dihedral : 6.304 79.492 965 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.30), residues: 846 helix: 0.28 (0.35), residues: 205 sheet: -0.23 (0.35), residues: 233 loop : -0.62 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 99 HIS 0.010 0.002 HIS A 80 PHE 0.018 0.002 PHE D 228 TYR 0.018 0.002 TYR A 325 ARG 0.006 0.001 ARG D 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.6026 (t80) cc_final: 0.5761 (t80) REVERT: A 133 MET cc_start: 0.8878 (ppp) cc_final: 0.8662 (ppp) REVERT: A 134 THR cc_start: 0.9516 (m) cc_final: 0.9157 (m) REVERT: A 214 PHE cc_start: 0.8382 (m-80) cc_final: 0.7670 (m-80) REVERT: A 272 MET cc_start: 0.8576 (ppp) cc_final: 0.8344 (ppp) REVERT: A 288 PHE cc_start: 0.9373 (m-10) cc_final: 0.9116 (m-80) REVERT: C 29 ASP cc_start: 0.8099 (t0) cc_final: 0.7671 (t0) REVERT: C 129 LEU cc_start: 0.9131 (mt) cc_final: 0.8902 (mt) REVERT: C 172 GLN cc_start: 0.8652 (mp-120) cc_final: 0.8004 (mp-120) REVERT: C 223 ASN cc_start: 0.8577 (t0) cc_final: 0.7936 (p0) REVERT: C 232 LYS cc_start: 0.8911 (tppt) cc_final: 0.8466 (tppt) REVERT: C 315 LEU cc_start: 0.9125 (mm) cc_final: 0.8897 (mm) REVERT: D 65 PHE cc_start: 0.7477 (m-80) cc_final: 0.7205 (m-80) REVERT: D 90 TYR cc_start: 0.7861 (m-10) cc_final: 0.7307 (m-80) REVERT: D 193 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7899 (ttt180) REVERT: D 209 MET cc_start: 0.6860 (mpp) cc_final: 0.6360 (mmm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1773 time to fit residues: 28.5702 Evaluate side-chains 91 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.106327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084912 restraints weight = 29574.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.087802 restraints weight = 18463.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089826 restraints weight = 13233.128| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6975 Z= 0.318 Angle : 0.744 9.754 9498 Z= 0.382 Chirality : 0.048 0.240 1086 Planarity : 0.006 0.059 1191 Dihedral : 6.658 80.299 965 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.30), residues: 846 helix: 0.01 (0.35), residues: 205 sheet: -0.48 (0.35), residues: 234 loop : -0.64 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 99 HIS 0.006 0.002 HIS C 353 PHE 0.026 0.003 PHE C 27 TYR 0.027 0.002 TYR D 52 ARG 0.006 0.001 ARG D 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.72 seconds wall clock time: 41 minutes 16.13 seconds (2476.13 seconds total)