Starting phenix.real_space_refine on Sat Jul 26 12:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jhj_22338/07_2025/7jhj_22338.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhj_22338/07_2025/7jhj_22338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jhj_22338/07_2025/7jhj_22338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhj_22338/07_2025/7jhj_22338.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhj_22338/07_2025/7jhj_22338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhj_22338/07_2025/7jhj_22338.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 66 5.16 5 C 5420 2.51 5 N 1434 2.21 5 O 1566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1715 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2532 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 364 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1757 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2083 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 268} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.63 Number of scatterers: 8486 At special positions: 0 Unit cell: (104.94, 115.54, 108.12, 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 66 16.00 O 1566 8.00 N 1434 7.00 C 5420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 97 " - pdb=" SG CYS R 174 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 14 sheets defined 33.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.808A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.504A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.680A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.751A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.003A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.529A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.522A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.606A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.946A pdb=" N LEU R 44 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU R 49 " --> pdb=" O VAL R 45 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 92 removed outlier: 3.629A pdb=" N VAL R 70 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 127 removed outlier: 3.631A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 161 removed outlier: 3.665A pdb=" N GLY R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 212 removed outlier: 3.667A pdb=" N LEU R 189 " --> pdb=" O ALA R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 220 removed outlier: 3.915A pdb=" N ARG R 219 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS R 220 " --> pdb=" O PHE R 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 216 through 220' Processing helix chain 'R' and resid 221 through 240 removed outlier: 4.067A pdb=" N VAL R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE R 233 " --> pdb=" O PHE R 229 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N CYS R 234 " --> pdb=" O THR R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 246 Processing helix chain 'R' and resid 267 through 285 removed outlier: 3.623A pdb=" N ALA R 271 " --> pdb=" O TYR R 267 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER R 285 " --> pdb=" O LEU R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 301 removed outlier: 3.544A pdb=" N SER R 292 " --> pdb=" O HIS R 288 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR R 298 " --> pdb=" O LYS R 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.798A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.248A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.713A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.130A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.862A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.694A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.787A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.787A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 182 through 183 removed outlier: 5.583A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 168 through 170 410 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1408 1.32 - 1.44: 2340 1.44 - 1.57: 4812 1.57 - 1.69: 4 1.69 - 1.82: 95 Bond restraints: 8659 Sorted by residual: bond pdb=" CAY Y01 R 401 " pdb=" OAW Y01 R 401 " ideal model delta sigma weight residual 1.332 1.427 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" CAP Y01 R 401 " pdb=" CAQ Y01 R 401 " ideal model delta sigma weight residual 1.541 1.606 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CBE Y01 R 401 " pdb=" CBI Y01 R 401 " ideal model delta sigma weight residual 1.550 1.497 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" CAS Y01 R 401 " pdb=" CBF Y01 R 401 " ideal model delta sigma weight residual 1.533 1.486 0.047 2.00e-02 2.50e+03 5.55e+00 bond pdb=" CBB Y01 R 401 " pdb=" CBE Y01 R 401 " ideal model delta sigma weight residual 1.535 1.582 -0.047 2.00e-02 2.50e+03 5.47e+00 ... (remaining 8654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11331 2.00 - 3.99: 357 3.99 - 5.99: 53 5.99 - 7.99: 16 7.99 - 9.99: 3 Bond angle restraints: 11760 Sorted by residual: angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" CA GLU B 130 " pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N TYR R 267 " pdb=" CA TYR R 267 " pdb=" C TYR R 267 " ideal model delta sigma weight residual 109.81 117.34 -7.53 2.21e+00 2.05e-01 1.16e+01 angle pdb=" CAM Y01 R 401 " pdb=" CAY Y01 R 401 " pdb=" OAW Y01 R 401 " ideal model delta sigma weight residual 111.19 121.18 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C ARG B 129 " pdb=" N GLU B 130 " pdb=" CA GLU B 130 " ideal model delta sigma weight residual 122.08 126.82 -4.74 1.47e+00 4.63e-01 1.04e+01 ... (remaining 11755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 4434 14.08 - 28.16: 551 28.16 - 42.23: 140 42.23 - 56.31: 26 56.31 - 70.39: 5 Dihedral angle restraints: 5156 sinusoidal: 1938 harmonic: 3218 Sorted by residual: dihedral pdb=" CA TYR R 267 " pdb=" C TYR R 267 " pdb=" N PRO R 268 " pdb=" CA PRO R 268 " ideal model delta harmonic sigma weight residual -180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLU A 8 " pdb=" C GLU A 8 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1077 0.067 - 0.134: 259 0.134 - 0.201: 29 0.201 - 0.268: 7 0.268 - 0.335: 1 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CBG Y01 R 401 " pdb=" CAQ Y01 R 401 " pdb=" CBD Y01 R 401 " pdb=" CBI Y01 R 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CBF Y01 R 401 " pdb=" CAS Y01 R 401 " pdb=" CBD Y01 R 401 " pdb=" CBH Y01 R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.67 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1370 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 243 " -0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO R 244 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO R 244 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 244 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 269 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO R 270 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 270 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 270 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 199 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C PHE A 199 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE A 199 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 200 " 0.017 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2406 2.80 - 3.32: 7200 3.32 - 3.85: 13980 3.85 - 4.37: 16549 4.37 - 4.90: 29452 Nonbonded interactions: 69587 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.273 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OG SER D 21 " model vdw 2.281 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.309 3.040 nonbonded pdb=" O TYR R 32 " pdb=" OH TYR R 266 " model vdw 2.310 3.040 ... (remaining 69582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.690 Find NCS groups from input model: 0.080 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.009 0.095 8663 Z= 0.387 Angle : 0.871 9.985 11768 Z= 0.463 Chirality : 0.057 0.335 1373 Planarity : 0.007 0.086 1474 Dihedral : 13.452 70.389 3070 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.45 % Allowed : 8.38 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.50 (0.21), residues: 1101 helix: -2.24 (0.20), residues: 360 sheet: -1.96 (0.27), residues: 288 loop : -2.46 (0.24), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP R 113 HIS 0.008 0.002 HIS R 136 PHE 0.024 0.003 PHE D 27 TYR 0.024 0.003 TYR B 105 ARG 0.005 0.001 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.12624 ( 406) hydrogen bonds : angle 6.13275 ( 1137) SS BOND : bond 0.00512 ( 4) SS BOND : angle 1.18896 ( 8) covalent geometry : bond 0.00905 ( 8659) covalent geometry : angle 0.87052 (11760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.926 Fit side-chains REVERT: A 247 MET cc_start: 0.8311 (mtp) cc_final: 0.8107 (mtm) REVERT: A 251 ASP cc_start: 0.7728 (t70) cc_final: 0.7427 (t0) REVERT: B 30 LEU cc_start: 0.8432 (tp) cc_final: 0.8084 (tp) REVERT: B 101 MET cc_start: 0.8886 (mtp) cc_final: 0.8634 (mtp) REVERT: B 127 LYS cc_start: 0.8884 (mttp) cc_final: 0.8627 (mtpt) REVERT: B 228 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7820 (p0) REVERT: B 301 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8489 (mtpp) outliers start: 4 outliers final: 1 residues processed: 167 average time/residue: 0.2749 time to fit residues: 58.8196 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109854 restraints weight = 11238.442| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.38 r_work: 0.3047 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8663 Z= 0.125 Angle : 0.532 5.985 11768 Z= 0.285 Chirality : 0.042 0.133 1373 Planarity : 0.004 0.064 1474 Dihedral : 5.473 51.752 1269 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.36 % Allowed : 14.27 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.99 (0.24), residues: 1101 helix: -0.14 (0.27), residues: 364 sheet: -1.78 (0.28), residues: 281 loop : -1.89 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 113 HIS 0.004 0.001 HIS A 195 PHE 0.018 0.001 PHE R 57 TYR 0.015 0.001 TYR D 178 ARG 0.002 0.000 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 406) hydrogen bonds : angle 4.46520 ( 1137) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.68018 ( 8) covalent geometry : bond 0.00278 ( 8659) covalent geometry : angle 0.53233 (11760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.989 Fit side-chains REVERT: A 24 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7813 (mtm110) REVERT: A 247 MET cc_start: 0.8553 (mtp) cc_final: 0.8332 (mtm) REVERT: A 251 ASP cc_start: 0.8204 (t70) cc_final: 0.7805 (t0) REVERT: A 304 GLN cc_start: 0.8773 (tt0) cc_final: 0.8513 (tt0) REVERT: A 345 LYS cc_start: 0.8582 (tttt) cc_final: 0.8170 (ttmt) REVERT: B 127 LYS cc_start: 0.8968 (mttp) cc_final: 0.8649 (mtpt) REVERT: B 186 ASP cc_start: 0.8256 (m-30) cc_final: 0.8035 (m-30) REVERT: B 301 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8557 (mtpp) REVERT: R 240 MET cc_start: 0.6607 (tmm) cc_final: 0.6315 (tmm) outliers start: 12 outliers final: 8 residues processed: 159 average time/residue: 0.2643 time to fit residues: 55.5818 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106255 restraints weight = 11409.815| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.22 r_work: 0.3069 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8663 Z= 0.148 Angle : 0.528 6.038 11768 Z= 0.279 Chirality : 0.042 0.144 1373 Planarity : 0.004 0.061 1474 Dihedral : 5.192 50.991 1267 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.49 % Allowed : 14.95 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.39 (0.25), residues: 1101 helix: 0.60 (0.29), residues: 363 sheet: -1.58 (0.28), residues: 288 loop : -1.65 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 113 HIS 0.004 0.001 HIS D 35 PHE 0.018 0.001 PHE R 57 TYR 0.013 0.001 TYR D 223 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 406) hydrogen bonds : angle 4.20615 ( 1137) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.63194 ( 8) covalent geometry : bond 0.00342 ( 8659) covalent geometry : angle 0.52831 (11760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.881 Fit side-chains REVERT: A 24 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7910 (mtm110) REVERT: A 247 MET cc_start: 0.8550 (mtp) cc_final: 0.8313 (mtm) REVERT: A 251 ASP cc_start: 0.8299 (t70) cc_final: 0.7980 (t0) REVERT: A 304 GLN cc_start: 0.8801 (tt0) cc_final: 0.8581 (tt0) REVERT: A 345 LYS cc_start: 0.8748 (tttt) cc_final: 0.8306 (ttmt) REVERT: B 127 LYS cc_start: 0.9085 (mttp) cc_final: 0.8695 (mtpt) REVERT: B 186 ASP cc_start: 0.8403 (m-30) cc_final: 0.8128 (m-30) REVERT: B 301 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8929 (mtpp) REVERT: R 167 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6830 (pp) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 0.2336 time to fit residues: 49.4877 Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 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 294 ASN ** B 32 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 = 0.3691 r_free = 0.3691 target = 0.142480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109819 restraints weight = 11253.690| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.29 r_work: 0.3053 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8663 Z= 0.129 Angle : 0.509 6.066 11768 Z= 0.269 Chirality : 0.042 0.134 1373 Planarity : 0.004 0.060 1474 Dihedral : 5.003 50.070 1267 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.83 % Allowed : 16.53 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1101 helix: 0.91 (0.29), residues: 370 sheet: -1.49 (0.28), residues: 288 loop : -1.48 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 113 HIS 0.002 0.001 HIS A 213 PHE 0.020 0.001 PHE R 57 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 406) hydrogen bonds : angle 4.04847 ( 1137) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.54595 ( 8) covalent geometry : bond 0.00295 ( 8659) covalent geometry : angle 0.50877 (11760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.909 Fit side-chains REVERT: A 24 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.7971 (mtm110) REVERT: A 247 MET cc_start: 0.8661 (mtp) cc_final: 0.8435 (mtm) REVERT: A 251 ASP cc_start: 0.8330 (t70) cc_final: 0.8026 (t0) REVERT: A 304 GLN cc_start: 0.8809 (tt0) cc_final: 0.8599 (tt0) REVERT: A 345 LYS cc_start: 0.8796 (tttt) cc_final: 0.8369 (ttmt) REVERT: B 127 LYS cc_start: 0.9056 (mttp) cc_final: 0.8680 (mtpt) REVERT: B 301 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8871 (mttp) REVERT: R 81 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8442 (tt) REVERT: R 167 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6865 (pp) outliers start: 25 outliers final: 16 residues processed: 155 average time/residue: 0.2209 time to fit residues: 46.3086 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 32 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 = 0.3693 r_free = 0.3693 target = 0.142612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109667 restraints weight = 11289.979| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.31 r_work: 0.3029 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8663 Z= 0.134 Angle : 0.522 7.864 11768 Z= 0.272 Chirality : 0.042 0.146 1373 Planarity : 0.004 0.059 1474 Dihedral : 4.903 49.558 1267 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.06 % Allowed : 17.21 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1101 helix: 1.12 (0.29), residues: 370 sheet: -1.44 (0.28), residues: 287 loop : -1.37 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 82 HIS 0.003 0.001 HIS D 35 PHE 0.020 0.001 PHE R 57 TYR 0.014 0.001 TYR D 223 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 406) hydrogen bonds : angle 4.00231 ( 1137) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.55191 ( 8) covalent geometry : bond 0.00310 ( 8659) covalent geometry : angle 0.52176 (11760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.892 Fit side-chains REVERT: A 24 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.7917 (mtm110) REVERT: A 247 MET cc_start: 0.8552 (mtp) cc_final: 0.8310 (mtm) REVERT: A 251 ASP cc_start: 0.8324 (t70) cc_final: 0.8029 (t0) REVERT: A 304 GLN cc_start: 0.8788 (tt0) cc_final: 0.8572 (tt0) REVERT: A 345 LYS cc_start: 0.8768 (tttt) cc_final: 0.8315 (ttmt) REVERT: B 59 TYR cc_start: 0.8892 (m-80) cc_final: 0.8630 (m-80) REVERT: B 61 MET cc_start: 0.8540 (ppp) cc_final: 0.8251 (ptm) REVERT: B 127 LYS cc_start: 0.9108 (mttp) cc_final: 0.8699 (mtpt) REVERT: B 186 ASP cc_start: 0.8513 (m-30) cc_final: 0.8193 (m-30) REVERT: B 301 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8610 (mtpp) REVERT: B 338 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8969 (mm) REVERT: R 167 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6690 (pp) outliers start: 27 outliers final: 18 residues processed: 155 average time/residue: 0.2213 time to fit residues: 46.3677 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 92 optimal weight: 0.0000 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111128 restraints weight = 11200.755| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.30 r_work: 0.3047 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8663 Z= 0.114 Angle : 0.511 8.825 11768 Z= 0.267 Chirality : 0.042 0.144 1373 Planarity : 0.003 0.059 1474 Dihedral : 4.730 48.320 1267 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.83 % Allowed : 18.01 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1101 helix: 1.30 (0.29), residues: 371 sheet: -1.27 (0.27), residues: 302 loop : -1.34 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 113 HIS 0.002 0.001 HIS A 213 PHE 0.021 0.001 PHE R 57 TYR 0.013 0.001 TYR D 223 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 406) hydrogen bonds : angle 3.91940 ( 1137) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.51367 ( 8) covalent geometry : bond 0.00258 ( 8659) covalent geometry : angle 0.51117 (11760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.915 Fit side-chains REVERT: A 24 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7927 (mtm110) REVERT: A 247 MET cc_start: 0.8626 (mtp) cc_final: 0.8393 (mtm) REVERT: A 251 ASP cc_start: 0.8315 (t70) cc_final: 0.7990 (t0) REVERT: A 345 LYS cc_start: 0.8762 (tttt) cc_final: 0.8325 (ttmt) REVERT: B 61 MET cc_start: 0.8526 (ppp) cc_final: 0.8270 (ppp) REVERT: B 127 LYS cc_start: 0.9075 (mttp) cc_final: 0.8677 (mtpt) REVERT: B 186 ASP cc_start: 0.8467 (m-30) cc_final: 0.8142 (m-30) REVERT: B 262 MET cc_start: 0.8771 (tpp) cc_final: 0.8507 (tpp) REVERT: B 301 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8700 (mtpp) REVERT: R 167 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6746 (pp) REVERT: R 244 PRO cc_start: 0.9018 (Cg_exo) cc_final: 0.8807 (Cg_endo) outliers start: 25 outliers final: 19 residues processed: 149 average time/residue: 0.2318 time to fit residues: 46.5398 Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110657 restraints weight = 11294.077| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.37 r_work: 0.3033 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8663 Z= 0.124 Angle : 0.517 7.725 11768 Z= 0.270 Chirality : 0.042 0.145 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.694 47.763 1267 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.94 % Allowed : 18.23 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.62 (0.26), residues: 1101 helix: 1.40 (0.29), residues: 371 sheet: -1.22 (0.27), residues: 302 loop : -1.33 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 113 HIS 0.003 0.001 HIS D 35 PHE 0.018 0.001 PHE R 57 TYR 0.014 0.001 TYR D 223 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 406) hydrogen bonds : angle 3.91428 ( 1137) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.54486 ( 8) covalent geometry : bond 0.00287 ( 8659) covalent geometry : angle 0.51739 (11760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.316 Fit side-chains REVERT: A 24 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7753 (mtm110) REVERT: A 247 MET cc_start: 0.8472 (mtp) cc_final: 0.8223 (mtm) REVERT: A 251 ASP cc_start: 0.8095 (t70) cc_final: 0.7780 (t0) REVERT: A 345 LYS cc_start: 0.8574 (tttt) cc_final: 0.8142 (ttmt) REVERT: B 61 MET cc_start: 0.8387 (ppp) cc_final: 0.8118 (ppp) REVERT: B 127 LYS cc_start: 0.8976 (mttp) cc_final: 0.8610 (mtpt) REVERT: B 186 ASP cc_start: 0.8324 (m-30) cc_final: 0.8028 (m-30) REVERT: B 262 MET cc_start: 0.8565 (tpp) cc_final: 0.8226 (tpp) REVERT: B 301 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8649 (mtpp) REVERT: B 338 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8863 (mm) REVERT: R 167 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6624 (pp) REVERT: R 244 PRO cc_start: 0.8982 (Cg_exo) cc_final: 0.8724 (Cg_endo) outliers start: 26 outliers final: 18 residues processed: 150 average time/residue: 0.2291 time to fit residues: 46.4587 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 105 optimal weight: 0.0370 chunk 81 optimal weight: 0.2980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 88 ASN B 259 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107439 restraints weight = 11354.816| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.23 r_work: 0.3061 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8663 Z= 0.135 Angle : 0.532 7.138 11768 Z= 0.279 Chirality : 0.042 0.149 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.704 47.594 1267 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.72 % Allowed : 19.48 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1101 helix: 1.42 (0.29), residues: 372 sheet: -1.22 (0.27), residues: 302 loop : -1.34 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 113 HIS 0.002 0.001 HIS D 35 PHE 0.022 0.001 PHE R 57 TYR 0.015 0.001 TYR D 223 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 406) hydrogen bonds : angle 3.97381 ( 1137) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.55755 ( 8) covalent geometry : bond 0.00317 ( 8659) covalent geometry : angle 0.53191 (11760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.910 Fit side-chains REVERT: A 24 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7897 (mtm110) REVERT: A 247 MET cc_start: 0.8595 (mtp) cc_final: 0.8357 (mtm) REVERT: A 251 ASP cc_start: 0.8292 (t70) cc_final: 0.7957 (t0) REVERT: A 345 LYS cc_start: 0.8740 (tttt) cc_final: 0.8307 (ttmt) REVERT: B 61 MET cc_start: 0.8536 (ppp) cc_final: 0.8252 (ppp) REVERT: B 127 LYS cc_start: 0.9055 (mttp) cc_final: 0.8665 (mtpt) REVERT: B 186 ASP cc_start: 0.8425 (m-30) cc_final: 0.8096 (m-30) REVERT: B 262 MET cc_start: 0.8760 (tpp) cc_final: 0.8438 (tpp) REVERT: B 301 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8666 (mtpp) REVERT: B 338 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8919 (mm) REVERT: R 116 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8355 (mm) REVERT: R 167 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6591 (pp) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.2370 time to fit residues: 46.3025 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 259 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110872 restraints weight = 11261.403| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.35 r_work: 0.3038 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8663 Z= 0.132 Angle : 0.529 6.690 11768 Z= 0.277 Chirality : 0.042 0.147 1373 Planarity : 0.003 0.058 1474 Dihedral : 4.672 47.303 1267 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.94 % Allowed : 19.71 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.54 (0.26), residues: 1101 helix: 1.49 (0.29), residues: 372 sheet: -1.15 (0.27), residues: 301 loop : -1.33 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 113 HIS 0.002 0.001 HIS D 35 PHE 0.021 0.001 PHE R 57 TYR 0.016 0.001 TYR D 223 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 406) hydrogen bonds : angle 3.95405 ( 1137) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.56301 ( 8) covalent geometry : bond 0.00308 ( 8659) covalent geometry : angle 0.52896 (11760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.914 Fit side-chains REVERT: A 24 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.7947 (mtm110) REVERT: A 247 MET cc_start: 0.8614 (mtp) cc_final: 0.8379 (mtm) REVERT: A 251 ASP cc_start: 0.8316 (t70) cc_final: 0.7989 (t0) REVERT: A 345 LYS cc_start: 0.8769 (tttt) cc_final: 0.8337 (ttmt) REVERT: B 61 MET cc_start: 0.8548 (ppp) cc_final: 0.8275 (ppp) REVERT: B 127 LYS cc_start: 0.9075 (mttp) cc_final: 0.8673 (mtpt) REVERT: B 186 ASP cc_start: 0.8448 (m-30) cc_final: 0.8111 (m-30) REVERT: B 220 GLN cc_start: 0.8679 (mt0) cc_final: 0.8471 (mt0) REVERT: B 262 MET cc_start: 0.8815 (tpp) cc_final: 0.8537 (tpp) REVERT: B 301 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8812 (mttp) REVERT: B 338 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8933 (mm) REVERT: R 116 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8377 (mm) REVERT: R 167 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6612 (pp) outliers start: 26 outliers final: 20 residues processed: 148 average time/residue: 0.2457 time to fit residues: 48.0382 Evaluate side-chains 153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107877 restraints weight = 11249.483| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.22 r_work: 0.3064 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8663 Z= 0.142 Angle : 0.540 6.433 11768 Z= 0.283 Chirality : 0.043 0.149 1373 Planarity : 0.003 0.058 1474 Dihedral : 4.720 47.383 1267 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.72 % Allowed : 19.82 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1101 helix: 1.52 (0.29), residues: 372 sheet: -1.14 (0.28), residues: 301 loop : -1.37 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 113 HIS 0.002 0.001 HIS D 35 PHE 0.021 0.001 PHE R 57 TYR 0.017 0.001 TYR D 223 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 406) hydrogen bonds : angle 3.99803 ( 1137) SS BOND : bond 0.00274 ( 4) SS BOND : angle 0.56300 ( 8) covalent geometry : bond 0.00335 ( 8659) covalent geometry : angle 0.53960 (11760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.914 Fit side-chains REVERT: A 24 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.7910 (mtm110) REVERT: A 247 MET cc_start: 0.8597 (mtp) cc_final: 0.8359 (mtm) REVERT: A 251 ASP cc_start: 0.8289 (t70) cc_final: 0.7956 (t0) REVERT: B 61 MET cc_start: 0.8499 (ppp) cc_final: 0.8211 (ppp) REVERT: B 127 LYS cc_start: 0.9050 (mttp) cc_final: 0.8659 (mtpt) REVERT: B 186 ASP cc_start: 0.8417 (m-30) cc_final: 0.8093 (m-30) REVERT: B 220 GLN cc_start: 0.8606 (mt0) cc_final: 0.8397 (mt0) REVERT: B 262 MET cc_start: 0.8764 (tpp) cc_final: 0.8492 (tpp) REVERT: B 301 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8803 (mttp) REVERT: B 338 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8916 (mm) REVERT: D 180 MET cc_start: 0.8995 (ttp) cc_final: 0.8744 (tmm) REVERT: R 116 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8362 (mm) REVERT: R 167 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6629 (pp) REVERT: R 284 TRP cc_start: 0.8616 (t60) cc_final: 0.8189 (t-100) outliers start: 24 outliers final: 21 residues processed: 144 average time/residue: 0.2462 time to fit residues: 46.6390 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0570 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111686 restraints weight = 11374.034| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.39 r_work: 0.3033 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8663 Z= 0.115 Angle : 0.520 6.201 11768 Z= 0.274 Chirality : 0.042 0.147 1373 Planarity : 0.003 0.058 1474 Dihedral : 4.604 46.562 1267 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.83 % Allowed : 19.59 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.42 (0.26), residues: 1101 helix: 1.61 (0.29), residues: 371 sheet: -1.05 (0.28), residues: 305 loop : -1.33 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 113 HIS 0.002 0.001 HIS D 35 PHE 0.021 0.001 PHE R 57 TYR 0.015 0.001 TYR D 223 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 406) hydrogen bonds : angle 3.96467 ( 1137) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.50471 ( 8) covalent geometry : bond 0.00265 ( 8659) covalent geometry : angle 0.52027 (11760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4936.68 seconds wall clock time: 85 minutes 44.34 seconds (5144.34 seconds total)