Starting phenix.real_space_refine on Tue Feb 13 08:23:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0u_26951/02_2024/7v0u_26951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0u_26951/02_2024/7v0u_26951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0u_26951/02_2024/7v0u_26951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0u_26951/02_2024/7v0u_26951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0u_26951/02_2024/7v0u_26951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0u_26951/02_2024/7v0u_26951.pdb" } resolution = 3.0 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= 0.257 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2839 2.51 5 N 777 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 316": "OD1" <-> "OD2" 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: 4453 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2268 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2183 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.97, per 1000 atoms: 0.67 Number of scatterers: 4453 At special positions: 0 Unit cell: (78.435, 65.985, 87.565, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 825 8.00 N 777 7.00 C 2839 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: 1.92 Conformation dependent library (CDL) restraints added in 868.1 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 42.8% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'F' and resid 103 through 116 removed outlier: 3.861A pdb=" N LYS F 116 " --> pdb=" O ARG F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 142 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 163 through 168 removed outlier: 4.123A pdb=" N GLU F 168 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 201 Processing helix chain 'F' and resid 277 through 291 Processing helix chain 'F' and resid 291 through 300 Processing helix chain 'F' and resid 303 through 317 removed outlier: 3.730A pdb=" N LEU F 307 " --> pdb=" O SER F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 334 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.533A pdb=" N GLY D 92 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.946A pdb=" N LYS D 116 " --> pdb=" O ARG D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 148 through 158 removed outlier: 4.625A pdb=" N GLU D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 171 removed outlier: 4.284A pdb=" N GLU D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 201 Processing helix chain 'D' and resid 277 through 291 Processing helix chain 'D' and resid 291 through 301 Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.904A pdb=" N LEU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 335 through 347 Processing sheet with id=AA1, first strand: chain 'F' and resid 85 through 87 removed outlier: 6.913A pdb=" N LEU F 61 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG F 80 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL F 59 " --> pdb=" O ARG F 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 118 through 123 removed outlier: 4.218A pdb=" N VAL F 119 " --> pdb=" O PHE F 244 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ARG F 246 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU F 121 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN F 248 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU F 123 " --> pdb=" O GLN F 248 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ALA F 250 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 12.146A pdb=" N GLY F 243 " --> pdb=" O GLY F 270 " (cutoff:3.500A) removed outlier: 11.441A pdb=" N GLY F 270 " --> pdb=" O GLY F 243 " (cutoff:3.500A) removed outlier: 12.448A pdb=" N VAL F 245 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N LEU F 268 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU F 247 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 11.850A pdb=" N PHE F 266 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N GLU F 249 " --> pdb=" O PHE F 264 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE F 264 " --> pdb=" O GLU F 249 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA F 226 " --> pdb=" O PHE F 264 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N PHE F 266 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU F 228 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU F 268 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU F 230 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLY F 270 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY F 232 " --> pdb=" O GLY F 270 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU F 60 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL F 231 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN F 62 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ARG F 233 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU F 64 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL F 59 " --> pdb=" O ARG F 80 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG F 80 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU F 61 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AA5, first strand: chain 'D' and resid 85 through 87 removed outlier: 6.892A pdb=" N LEU D 61 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG D 80 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 59 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS D 56 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR D 227 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR D 58 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL D 229 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU D 60 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL D 231 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN D 62 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ARG D 233 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU D 64 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE D 262 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA D 226 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 264 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG D 263 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR D 118 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ARG D 246 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU D 120 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN D 248 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP D 122 " --> pdb=" O GLN D 248 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N ALA D 250 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 85 through 87 removed outlier: 6.892A pdb=" N LEU D 61 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG D 80 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 59 " --> pdb=" O ARG D 80 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 561 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: 1.24 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 809 1.32 - 1.44: 1076 1.44 - 1.56: 2635 1.56 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4540 Sorted by residual: bond pdb=" C PRO D 271 " pdb=" O PRO D 271 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.18e-02 7.18e+03 7.89e+00 bond pdb=" N LEU D 178 " pdb=" CA LEU D 178 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.64e+00 bond pdb=" CA ALA D 234 " pdb=" CB ALA D 234 " ideal model delta sigma weight residual 1.530 1.493 0.038 1.50e-02 4.44e+03 6.25e+00 bond pdb=" CA ALA D 176 " pdb=" CB ALA D 176 " ideal model delta sigma weight residual 1.533 1.492 0.041 1.66e-02 3.63e+03 6.04e+00 bond pdb=" N VAL D 177 " pdb=" CA VAL D 177 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.17e-02 7.31e+03 6.03e+00 ... (remaining 4535 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 188 107.22 - 113.92: 2555 113.92 - 120.61: 1759 120.61 - 127.31: 1601 127.31 - 134.00: 58 Bond angle restraints: 6161 Sorted by residual: angle pdb=" N ALA D 176 " pdb=" CA ALA D 176 " pdb=" C ALA D 176 " ideal model delta sigma weight residual 108.76 116.18 -7.42 1.58e+00 4.01e-01 2.21e+01 angle pdb=" N ARG D 180 " pdb=" CA ARG D 180 " pdb=" C ARG D 180 " ideal model delta sigma weight residual 110.23 103.66 6.57 1.45e+00 4.76e-01 2.05e+01 angle pdb=" CA ARG D 180 " pdb=" C ARG D 180 " pdb=" O ARG D 180 " ideal model delta sigma weight residual 121.19 116.50 4.69 1.10e+00 8.26e-01 1.82e+01 angle pdb=" N GLU D 238 " pdb=" CA GLU D 238 " pdb=" C GLU D 238 " ideal model delta sigma weight residual 112.90 108.10 4.80 1.31e+00 5.83e-01 1.35e+01 angle pdb=" C LEU D 269 " pdb=" N GLY D 270 " pdb=" CA GLY D 270 " ideal model delta sigma weight residual 121.87 116.37 5.50 1.57e+00 4.06e-01 1.23e+01 ... (remaining 6156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 2316 18.11 - 36.21: 292 36.21 - 54.32: 109 54.32 - 72.43: 32 72.43 - 90.53: 17 Dihedral angle restraints: 2766 sinusoidal: 1149 harmonic: 1617 Sorted by residual: dihedral pdb=" CA TRP F 81 " pdb=" C TRP F 81 " pdb=" N VAL F 82 " pdb=" CA VAL F 82 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL D 65 " pdb=" C VAL D 65 " pdb=" N MET D 66 " pdb=" CA MET D 66 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB GLU D 312 " pdb=" CG GLU D 312 " pdb=" CD GLU D 312 " pdb=" OE1 GLU D 312 " ideal model delta sinusoidal sigma weight residual 0.00 90.53 -90.53 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 2763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 535 0.047 - 0.094: 126 0.094 - 0.141: 31 0.141 - 0.188: 8 0.188 - 0.235: 3 Chirality restraints: 703 Sorted by residual: chirality pdb=" CA VAL D 177 " pdb=" N VAL D 177 " pdb=" C VAL D 177 " pdb=" CB VAL D 177 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA GLU D 238 " pdb=" N GLU D 238 " pdb=" C GLU D 238 " pdb=" CB GLU D 238 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU D 99 " pdb=" CB LEU D 99 " pdb=" CD1 LEU D 99 " pdb=" CD2 LEU D 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 700 not shown) Planarity restraints: 805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 273 " 0.043 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO F 274 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 274 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 274 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 220 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO D 221 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 231 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL D 231 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL D 231 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY D 232 " 0.009 2.00e-02 2.50e+03 ... (remaining 802 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 728 2.77 - 3.30: 4044 3.30 - 3.83: 7770 3.83 - 4.37: 9213 4.37 - 4.90: 15623 Nonbonded interactions: 37378 Sorted by model distance: nonbonded pdb=" OE2 GLU D 77 " pdb=" ND1 HIS D 163 " model vdw 2.232 2.520 nonbonded pdb=" O PRO F 221 " pdb=" OG SER F 224 " model vdw 2.234 2.440 nonbonded pdb=" NH2 ARG D 246 " pdb=" O ALA D 301 " model vdw 2.254 2.520 nonbonded pdb=" OH TYR F 58 " pdb=" O HOH F1001 " model vdw 2.269 2.440 nonbonded pdb=" O ALA F 286 " pdb=" OG SER F 290 " model vdw 2.333 2.440 ... (remaining 37373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 54 through 203 or resid 217 through 348)) selection = (chain 'F' and (resid 54 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 181 or resid 192 through 348)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.080 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.420 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 0.046 4540 Z= 0.335 Angle : 0.751 8.628 6161 Z= 0.427 Chirality : 0.048 0.235 703 Planarity : 0.006 0.064 805 Dihedral : 20.370 90.533 1710 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.50 % Allowed : 27.08 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.35), residues: 548 helix: 0.68 (0.34), residues: 216 sheet: 0.96 (0.54), residues: 106 loop : 0.02 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 75 HIS 0.008 0.001 HIS D 101 PHE 0.016 0.002 PHE D 314 TYR 0.014 0.002 TYR F 58 ARG 0.013 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.525 Fit side-chains REVERT: D 238 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6754 (tp30) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 1.4875 time to fit residues: 124.3021 Evaluate side-chains 75 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 260 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4540 Z= 0.265 Angle : 0.555 6.389 6161 Z= 0.283 Chirality : 0.041 0.159 703 Planarity : 0.004 0.041 805 Dihedral : 6.166 49.916 622 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.79 % Allowed : 23.33 % Favored : 71.88 % 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: 0.92 (0.35), residues: 548 helix: 1.12 (0.35), residues: 216 sheet: 1.04 (0.53), residues: 106 loop : 0.02 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.003 0.001 HIS D 101 PHE 0.013 0.002 PHE D 314 TYR 0.014 0.002 TYR D 278 ARG 0.006 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 0.523 Fit side-chains REVERT: F 86 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: F 125 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 199 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8240 (mm) REVERT: F 281 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8818 (mp) REVERT: F 291 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: D 63 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: D 116 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8625 (ptmt) REVERT: D 291 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7231 (tt0) outliers start: 23 outliers final: 7 residues processed: 83 average time/residue: 1.2866 time to fit residues: 110.6187 Evaluate side-chains 84 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 291 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 ASN D 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 4540 Z= 0.377 Angle : 0.603 6.174 6161 Z= 0.303 Chirality : 0.042 0.152 703 Planarity : 0.005 0.038 805 Dihedral : 4.722 38.243 604 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.42 % Allowed : 22.50 % Favored : 72.08 % 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: 0.75 (0.35), residues: 548 helix: 1.00 (0.35), residues: 216 sheet: 0.96 (0.55), residues: 101 loop : -0.07 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 81 HIS 0.004 0.001 HIS D 309 PHE 0.015 0.002 PHE D 314 TYR 0.016 0.002 TYR D 278 ARG 0.004 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 0.585 Fit side-chains REVERT: F 86 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: F 125 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8327 (mm-30) REVERT: F 199 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8293 (mm) REVERT: F 281 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (mp) REVERT: F 291 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8609 (tm-30) REVERT: D 63 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: D 116 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8708 (ptmt) REVERT: D 216 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.6017 (mt) REVERT: D 291 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7264 (tt0) outliers start: 26 outliers final: 10 residues processed: 85 average time/residue: 1.4366 time to fit residues: 126.0526 Evaluate side-chains 83 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 291 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 26 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- 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: 0.8420 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4540 Z= 0.290 Angle : 0.543 4.964 6161 Z= 0.276 Chirality : 0.040 0.147 703 Planarity : 0.004 0.037 805 Dihedral : 4.547 37.356 604 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.00 % Allowed : 22.92 % Favored : 72.08 % 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: 0.89 (0.36), residues: 548 helix: 1.22 (0.35), residues: 216 sheet: 0.85 (0.56), residues: 103 loop : -0.02 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.004 0.001 HIS D 309 PHE 0.015 0.002 PHE D 314 TYR 0.014 0.002 TYR D 278 ARG 0.003 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 0.533 Fit side-chains REVERT: F 86 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: F 199 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8238 (mm) REVERT: F 281 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8820 (mp) REVERT: F 291 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: F 292 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7845 (ttp80) REVERT: D 63 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7097 (mt-10) REVERT: D 216 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.6044 (mt) outliers start: 24 outliers final: 10 residues processed: 88 average time/residue: 1.4567 time to fit residues: 132.1719 Evaluate side-chains 85 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 291 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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: 0.8461 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4540 Z= 0.421 Angle : 0.645 7.244 6161 Z= 0.321 Chirality : 0.043 0.142 703 Planarity : 0.005 0.041 805 Dihedral : 4.970 41.504 604 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.83 % Allowed : 24.17 % Favored : 70.00 % 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 (0.35), residues: 548 helix: 1.03 (0.35), residues: 216 sheet: 0.85 (0.52), residues: 111 loop : -0.16 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 75 HIS 0.005 0.001 HIS D 309 PHE 0.017 0.002 PHE F 314 TYR 0.017 0.002 TYR D 278 ARG 0.003 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 69 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: F 86 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: F 199 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8326 (mm) REVERT: F 281 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8813 (mp) REVERT: F 291 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: D 63 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: D 216 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6124 (mt) REVERT: D 291 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: D 348 GLN cc_start: 0.6266 (OUTLIER) cc_final: 0.6009 (tt0) outliers start: 28 outliers final: 10 residues processed: 88 average time/residue: 1.5106 time to fit residues: 137.0192 Evaluate side-chains 85 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 348 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.8417 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4540 Z= 0.200 Angle : 0.510 5.197 6161 Z= 0.259 Chirality : 0.039 0.142 703 Planarity : 0.004 0.040 805 Dihedral : 4.489 38.231 604 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.75 % Allowed : 25.42 % Favored : 70.83 % 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 (0.36), residues: 548 helix: 1.41 (0.36), residues: 216 sheet: 0.83 (0.52), residues: 115 loop : 0.04 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.003 0.001 HIS D 163 PHE 0.014 0.001 PHE D 314 TYR 0.011 0.002 TYR D 278 ARG 0.003 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.518 Fit side-chains REVERT: F 86 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: F 155 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.6601 (ttt90) REVERT: F 199 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8213 (mm) REVERT: F 291 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: F 297 ASP cc_start: 0.8054 (m-30) cc_final: 0.7808 (m-30) REVERT: D 63 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: D 216 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.6044 (mt) REVERT: D 348 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5981 (tt0) outliers start: 18 outliers final: 9 residues processed: 87 average time/residue: 1.4630 time to fit residues: 131.2632 Evaluate side-chains 88 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 348 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8401 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4540 Z= 0.176 Angle : 0.495 9.873 6161 Z= 0.247 Chirality : 0.038 0.141 703 Planarity : 0.004 0.038 805 Dihedral : 4.195 35.459 604 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.79 % Allowed : 24.79 % Favored : 70.42 % 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: 1.31 (0.36), residues: 548 helix: 1.61 (0.35), residues: 216 sheet: 0.98 (0.52), residues: 115 loop : 0.16 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 81 HIS 0.003 0.001 HIS D 101 PHE 0.014 0.001 PHE D 314 TYR 0.009 0.001 TYR F 278 ARG 0.003 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.599 Fit side-chains REVERT: F 86 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: F 155 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6539 (ttt90) REVERT: F 199 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8145 (mm) REVERT: F 297 ASP cc_start: 0.8040 (m-30) cc_final: 0.7798 (m-30) REVERT: D 63 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: D 216 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.6062 (mt) REVERT: D 348 GLN cc_start: 0.6168 (OUTLIER) cc_final: 0.5952 (tt0) outliers start: 23 outliers final: 9 residues processed: 88 average time/residue: 1.3110 time to fit residues: 119.3482 Evaluate side-chains 86 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 348 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4540 Z= 0.149 Angle : 0.477 7.151 6161 Z= 0.237 Chirality : 0.038 0.140 703 Planarity : 0.004 0.037 805 Dihedral : 3.994 33.257 604 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.96 % Allowed : 25.83 % Favored : 70.21 % 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: 1.52 (0.36), residues: 548 helix: 1.81 (0.36), residues: 216 sheet: 1.35 (0.55), residues: 106 loop : 0.12 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 81 HIS 0.003 0.001 HIS D 101 PHE 0.013 0.001 PHE D 314 TYR 0.009 0.002 TYR F 278 ARG 0.002 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.525 Fit side-chains REVERT: F 86 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: F 155 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6497 (ttt90) REVERT: F 199 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8086 (mm) REVERT: F 297 ASP cc_start: 0.7999 (m-30) cc_final: 0.7764 (m-30) REVERT: D 63 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7089 (mt-10) REVERT: D 66 MET cc_start: 0.7108 (ptm) cc_final: 0.6764 (ptt) REVERT: D 348 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.5893 (tt0) outliers start: 19 outliers final: 10 residues processed: 88 average time/residue: 1.3582 time to fit residues: 123.5575 Evaluate side-chains 86 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 348 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.8411 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4540 Z= 0.230 Angle : 0.538 11.353 6161 Z= 0.262 Chirality : 0.039 0.156 703 Planarity : 0.004 0.039 805 Dihedral : 4.169 35.144 604 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.17 % Allowed : 26.46 % Favored : 69.38 % 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: 1.47 (0.36), residues: 548 helix: 1.76 (0.35), residues: 216 sheet: 1.46 (0.54), residues: 104 loop : 0.04 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 81 HIS 0.004 0.001 HIS D 101 PHE 0.015 0.002 PHE D 314 TYR 0.012 0.002 TYR F 278 ARG 0.003 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.528 Fit side-chains REVERT: F 86 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: F 155 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.6597 (ttt90) REVERT: F 199 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8138 (mm) REVERT: F 291 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8542 (tm-30) REVERT: F 297 ASP cc_start: 0.8014 (m-30) cc_final: 0.7782 (m-30) REVERT: D 63 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: D 216 ILE cc_start: 0.6280 (OUTLIER) cc_final: 0.6077 (mt) REVERT: D 348 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5938 (tt0) outliers start: 20 outliers final: 10 residues processed: 85 average time/residue: 1.4781 time to fit residues: 129.6772 Evaluate side-chains 88 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 348 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8424 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4540 Z= 0.273 Angle : 0.563 9.137 6161 Z= 0.276 Chirality : 0.040 0.162 703 Planarity : 0.004 0.039 805 Dihedral : 4.323 36.891 604 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.75 % Allowed : 26.88 % Favored : 69.38 % 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: 1.37 (0.36), residues: 548 helix: 1.66 (0.35), residues: 216 sheet: 1.38 (0.54), residues: 104 loop : 0.02 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.004 0.001 HIS D 101 PHE 0.015 0.002 PHE D 314 TYR 0.012 0.002 TYR F 278 ARG 0.006 0.000 ARG D 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.485 Fit side-chains REVERT: F 86 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: F 155 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.6607 (ttt90) REVERT: F 199 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8166 (mm) REVERT: F 291 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8689 (tm-30) REVERT: F 297 ASP cc_start: 0.8023 (m-30) cc_final: 0.7787 (m-30) REVERT: D 63 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: D 216 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.6103 (mt) REVERT: D 348 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5974 (tt0) outliers start: 18 outliers final: 11 residues processed: 84 average time/residue: 1.3541 time to fit residues: 117.6417 Evaluate side-chains 90 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 348 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.155718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.121388 restraints weight = 4582.256| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.24 r_work: 0.2983 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4540 Z= 0.207 Angle : 0.522 8.463 6161 Z= 0.257 Chirality : 0.039 0.154 703 Planarity : 0.004 0.038 805 Dihedral : 4.206 36.131 604 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.96 % Allowed : 26.67 % Favored : 69.38 % 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: 1.42 (0.36), residues: 548 helix: 1.73 (0.35), residues: 216 sheet: 1.15 (0.50), residues: 118 loop : 0.09 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 81 HIS 0.003 0.001 HIS D 163 PHE 0.014 0.001 PHE D 314 TYR 0.011 0.002 TYR F 278 ARG 0.003 0.000 ARG D 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.38 seconds wall clock time: 49 minutes 3.68 seconds (2943.68 seconds total)