Starting phenix.real_space_refine on Wed Feb 14 02:59:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/02_2024/7jhj_22338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/02_2024/7jhj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/02_2024/7jhj_22338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/02_2024/7jhj_22338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/02_2024/7jhj_22338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/02_2024/7jhj_22338.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R ARG 219": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 5 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: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2118 Unusual residues: {'Y01': 1} Classifications: {'peptide': 277, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 268, None: 1} Not linked: pdbres="PHE R 304 " pdbres="Y01 R 401 " 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 Time building chain proxies: 5.28, per 1000 atoms: 0.62 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 - 3.50 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: 2.98 Conformation dependent library (CDL) restraints added in 1.6 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: 0.91 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: 2.38 Time building geometry restraints manager: 3.26 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: 95.96 - 103.61: 90 103.61 - 111.26: 3563 111.26 - 118.91: 3408 118.91 - 126.57: 4567 126.57 - 134.22: 132 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 2.440 nonbonded pdb=" OG SER D 7 " pdb=" OG SER D 21 " model vdw 2.281 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.309 2.440 nonbonded pdb=" O TYR R 32 " pdb=" OH TYR R 266 " model vdw 2.310 2.440 ... (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 ========== 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: 0.860 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: 2.650 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.560 Find NCS groups from input model: 0.270 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- 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 8659 Z= 0.594 Angle : 0.871 9.985 11760 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 0.991 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: 0.2705 time to fit residues: 57.9648 Evaluate side-chains 136 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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: 0.0030 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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** D 39 GLN D 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8659 Z= 0.136 Angle : 0.493 6.175 11760 Z= 0.263 Chirality : 0.040 0.133 1373 Planarity : 0.004 0.063 1474 Dihedral : 5.297 51.022 1269 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 1.47 % Allowed : 14.16 % 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: -2.03 (0.24), residues: 1101 helix: -0.15 (0.27), residues: 364 sheet: -1.80 (0.27), residues: 287 loop : -1.92 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 113 HIS 0.004 0.001 HIS A 195 PHE 0.018 0.001 PHE R 57 TYR 0.017 0.001 TYR D 178 ARG 0.002 0.000 ARG D 38 *********************** 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 170 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.001 Fit side-chains REVERT: A 24 ARG cc_start: 0.8046 (ttp-110) cc_final: 0.7703 (mtm110) REVERT: A 251 ASP cc_start: 0.7770 (t70) cc_final: 0.7365 (t0) REVERT: A 304 GLN cc_start: 0.8730 (tt0) cc_final: 0.8484 (tt0) REVERT: A 313 ARG cc_start: 0.8242 (mpt-90) cc_final: 0.7867 (ptp-170) REVERT: B 127 LYS cc_start: 0.8743 (mttp) cc_final: 0.8536 (mtpt) REVERT: B 228 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7786 (p0) REVERT: R 240 MET cc_start: 0.6445 (tmm) cc_final: 0.6174 (tmm) outliers start: 13 outliers final: 9 residues processed: 164 average time/residue: 0.2581 time to fit residues: 55.2374 Evaluate side-chains 152 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN 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 B residue 228 ASP 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 55 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8659 Z= 0.413 Angle : 0.605 6.741 11760 Z= 0.316 Chirality : 0.045 0.154 1373 Planarity : 0.004 0.062 1474 Dihedral : 5.626 52.220 1269 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 3.28 % Allowed : 14.38 % Favored : 82.33 % 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: -1.56 (0.25), residues: 1101 helix: 0.47 (0.29), residues: 362 sheet: -1.67 (0.27), residues: 293 loop : -1.76 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 113 HIS 0.005 0.001 HIS R 136 PHE 0.018 0.002 PHE R 57 TYR 0.021 0.002 TYR B 105 ARG 0.002 0.000 ARG B 219 *********************** 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 166 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.979 Fit side-chains REVERT: A 251 ASP cc_start: 0.7790 (t70) cc_final: 0.7455 (t0) REVERT: B 127 LYS cc_start: 0.8986 (mttp) cc_final: 0.8684 (mtpt) REVERT: B 228 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7788 (p0) REVERT: R 167 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7069 (pp) outliers start: 29 outliers final: 19 residues processed: 157 average time/residue: 0.2504 time to fit residues: 51.8419 Evaluate side-chains 152 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU 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 97 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 294 ASN A 331 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8659 Z= 0.174 Angle : 0.492 6.191 11760 Z= 0.259 Chirality : 0.041 0.147 1373 Planarity : 0.004 0.060 1474 Dihedral : 5.077 50.534 1269 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 2.04 % Allowed : 17.21 % Favored : 80.75 % 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: -1.09 (0.25), residues: 1101 helix: 0.96 (0.29), residues: 363 sheet: -1.46 (0.28), residues: 284 loop : -1.55 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 113 HIS 0.002 0.001 HIS D 35 PHE 0.019 0.001 PHE R 57 TYR 0.013 0.001 TYR D 178 ARG 0.002 0.000 ARG R 175 *********************** 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 164 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.041 Fit side-chains REVERT: A 24 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7687 (mtm110) REVERT: A 251 ASP cc_start: 0.7737 (t70) cc_final: 0.7398 (t0) REVERT: B 127 LYS cc_start: 0.8803 (mttp) cc_final: 0.8563 (mtpt) REVERT: B 228 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7772 (p0) REVERT: R 167 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6864 (pp) outliers start: 18 outliers final: 10 residues processed: 158 average time/residue: 0.2368 time to fit residues: 49.8348 Evaluate side-chains 149 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 304 GLN B 32 GLN B 183 HIS D 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8659 Z= 0.469 Angle : 0.642 8.706 11760 Z= 0.331 Chirality : 0.046 0.154 1373 Planarity : 0.004 0.060 1474 Dihedral : 5.595 52.881 1269 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 3.51 % Allowed : 16.76 % 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: -1.13 (0.25), residues: 1101 helix: 0.87 (0.29), residues: 362 sheet: -1.44 (0.29), residues: 278 loop : -1.55 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 82 HIS 0.005 0.001 HIS B 62 PHE 0.020 0.002 PHE R 57 TYR 0.022 0.002 TYR D 223 ARG 0.003 0.000 ARG B 251 *********************** 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 167 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 0.997 Fit side-chains REVERT: A 251 ASP cc_start: 0.7813 (t70) cc_final: 0.7499 (t0) REVERT: B 228 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7834 (p0) REVERT: B 301 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8531 (mtpp) REVERT: B 338 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8847 (mm) REVERT: R 167 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7059 (pp) outliers start: 31 outliers final: 19 residues processed: 158 average time/residue: 0.2431 time to fit residues: 50.8411 Evaluate side-chains 153 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.0040 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8659 Z= 0.139 Angle : 0.494 7.780 11760 Z= 0.256 Chirality : 0.041 0.139 1373 Planarity : 0.003 0.061 1474 Dihedral : 4.870 50.342 1269 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 2.83 % Allowed : 17.89 % Favored : 79.28 % 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: -0.74 (0.26), residues: 1101 helix: 1.30 (0.29), residues: 364 sheet: -1.35 (0.28), residues: 289 loop : -1.33 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 82 HIS 0.002 0.001 HIS B 91 PHE 0.017 0.001 PHE R 57 TYR 0.014 0.001 TYR D 178 ARG 0.002 0.000 ARG B 251 *********************** 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 168 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 0.962 Fit side-chains REVERT: A 24 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7718 (mtm110) REVERT: A 251 ASP cc_start: 0.7735 (t70) cc_final: 0.7408 (t0) REVERT: B 105 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8592 (t80) REVERT: B 127 LYS cc_start: 0.8827 (mttm) cc_final: 0.8583 (mtpt) REVERT: B 186 ASP cc_start: 0.7971 (m-30) cc_final: 0.7749 (m-30) REVERT: B 228 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7735 (p0) REVERT: B 338 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8771 (mm) REVERT: C 48 ASP cc_start: 0.8447 (t0) cc_final: 0.8219 (t0) REVERT: R 167 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6811 (pp) REVERT: R 174 CYS cc_start: 0.5841 (m) cc_final: 0.5547 (m) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 0.2398 time to fit residues: 51.6351 Evaluate side-chains 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU 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 153 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8659 Z= 0.171 Angle : 0.514 6.788 11760 Z= 0.264 Chirality : 0.042 0.170 1373 Planarity : 0.003 0.060 1474 Dihedral : 4.771 49.380 1269 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 3.17 % Allowed : 18.69 % Favored : 78.14 % 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: -0.60 (0.26), residues: 1101 helix: 1.42 (0.29), residues: 366 sheet: -1.28 (0.28), residues: 291 loop : -1.24 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 82 HIS 0.002 0.001 HIS D 35 PHE 0.021 0.001 PHE R 57 TYR 0.013 0.001 TYR D 223 ARG 0.002 0.000 ARG B 251 *********************** 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 173 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 0.995 Fit side-chains REVERT: A 24 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7708 (mtm110) REVERT: A 251 ASP cc_start: 0.7709 (t70) cc_final: 0.7400 (t0) REVERT: A 313 ARG cc_start: 0.8312 (mpt-90) cc_final: 0.7861 (ptp-170) REVERT: B 105 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8631 (t80) REVERT: B 127 LYS cc_start: 0.8818 (mttm) cc_final: 0.8566 (mtpt) REVERT: B 186 ASP cc_start: 0.7894 (m-30) cc_final: 0.7656 (m-30) REVERT: B 228 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7755 (p0) REVERT: C 48 ASP cc_start: 0.8463 (t0) cc_final: 0.8223 (t0) REVERT: R 140 CYS cc_start: 0.7487 (m) cc_final: 0.7274 (m) REVERT: R 167 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6859 (pp) outliers start: 28 outliers final: 18 residues processed: 163 average time/residue: 0.2261 time to fit residues: 49.2773 Evaluate side-chains 153 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU 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 153 LEU 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 62 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.0570 chunk 91 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 304 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8659 Z= 0.235 Angle : 0.545 8.709 11760 Z= 0.279 Chirality : 0.043 0.164 1373 Planarity : 0.004 0.060 1474 Dihedral : 4.866 49.435 1269 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 3.17 % Allowed : 18.46 % Favored : 78.37 % 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: -0.56 (0.26), residues: 1101 helix: 1.44 (0.29), residues: 365 sheet: -1.25 (0.28), residues: 291 loop : -1.22 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 82 HIS 0.003 0.001 HIS D 35 PHE 0.023 0.002 PHE R 57 TYR 0.017 0.001 TYR D 223 ARG 0.002 0.000 ARG B 251 *********************** 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 163 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.897 Fit side-chains REVERT: A 251 ASP cc_start: 0.7732 (t70) cc_final: 0.7431 (t0) REVERT: B 105 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8670 (t80) REVERT: B 127 LYS cc_start: 0.8854 (mttm) cc_final: 0.8584 (mtpt) REVERT: B 186 ASP cc_start: 0.7876 (m-30) cc_final: 0.7659 (m-30) REVERT: B 228 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7766 (p0) REVERT: B 301 LYS cc_start: 0.8807 (mtpp) cc_final: 0.8511 (mtpp) REVERT: B 338 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8792 (mm) REVERT: C 48 ASP cc_start: 0.8467 (t0) cc_final: 0.8228 (t0) REVERT: R 116 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8004 (mm) REVERT: R 140 CYS cc_start: 0.7581 (m) cc_final: 0.7370 (m) REVERT: R 167 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6882 (pp) REVERT: R 173 MET cc_start: 0.6826 (ttp) cc_final: 0.6418 (ptt) REVERT: R 174 CYS cc_start: 0.5713 (m) cc_final: 0.5362 (m) outliers start: 28 outliers final: 20 residues processed: 155 average time/residue: 0.2426 time to fit residues: 49.7494 Evaluate side-chains 155 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU 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 153 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 311 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8659 Z= 0.264 Angle : 0.552 6.492 11760 Z= 0.286 Chirality : 0.043 0.153 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.973 49.641 1269 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 3.40 % Allowed : 18.57 % Favored : 78.03 % 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: -0.58 (0.26), residues: 1101 helix: 1.42 (0.29), residues: 365 sheet: -1.26 (0.28), residues: 291 loop : -1.23 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 113 HIS 0.003 0.001 HIS R 136 PHE 0.021 0.002 PHE R 57 TYR 0.020 0.001 TYR D 223 ARG 0.002 0.000 ARG B 251 *********************** 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 162 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 0.976 Fit side-chains REVERT: A 247 MET cc_start: 0.8290 (mtp) cc_final: 0.8087 (mtm) REVERT: A 251 ASP cc_start: 0.7755 (t70) cc_final: 0.7458 (t0) REVERT: B 105 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8684 (t80) REVERT: B 127 LYS cc_start: 0.8885 (mttm) cc_final: 0.8598 (mtpt) REVERT: B 186 ASP cc_start: 0.7900 (m-30) cc_final: 0.7694 (m-30) REVERT: B 228 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7772 (p0) REVERT: B 301 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8518 (mtpp) REVERT: B 338 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8806 (mm) REVERT: C 48 ASP cc_start: 0.8455 (t0) cc_final: 0.8216 (t0) REVERT: R 116 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8314 (mm) REVERT: R 140 CYS cc_start: 0.7405 (m) cc_final: 0.7189 (m) REVERT: R 167 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6902 (pp) REVERT: R 174 CYS cc_start: 0.5755 (m) cc_final: 0.5402 (m) REVERT: R 175 ARG cc_start: 0.8034 (ptt90) cc_final: 0.7564 (ptt90) outliers start: 30 outliers final: 24 residues processed: 153 average time/residue: 0.2407 time to fit residues: 48.8121 Evaluate side-chains 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU 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 148 CYS 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 242 SER 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 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.0040 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8659 Z= 0.146 Angle : 0.509 6.272 11760 Z= 0.263 Chirality : 0.042 0.161 1373 Planarity : 0.003 0.059 1474 Dihedral : 4.649 47.345 1269 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 2.94 % Allowed : 18.80 % Favored : 78.26 % 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: -0.34 (0.26), residues: 1101 helix: 1.61 (0.29), residues: 365 sheet: -1.01 (0.29), residues: 285 loop : -1.17 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 82 HIS 0.002 0.001 HIS D 35 PHE 0.022 0.001 PHE R 57 TYR 0.015 0.001 TYR D 178 ARG 0.005 0.000 ARG A 313 ********************** 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 164 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 0.970 Fit side-chains REVERT: A 24 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7712 (mtm110) REVERT: A 251 ASP cc_start: 0.7698 (t70) cc_final: 0.7409 (t0) REVERT: B 105 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8684 (t80) REVERT: B 127 LYS cc_start: 0.8782 (mttm) cc_final: 0.8558 (mtpt) REVERT: B 228 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7748 (p0) REVERT: B 301 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8473 (mtpp) REVERT: R 116 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7924 (mm) REVERT: R 140 CYS cc_start: 0.7302 (m) cc_final: 0.7091 (m) REVERT: R 167 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6821 (pp) REVERT: R 175 ARG cc_start: 0.7945 (ptt90) cc_final: 0.7503 (ptt90) outliers start: 26 outliers final: 20 residues processed: 155 average time/residue: 0.2327 time to fit residues: 48.0326 Evaluate side-chains 153 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU 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 153 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.0970 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.0370 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.0770 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115211 restraints weight = 11145.217| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.34 r_work: 0.3111 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8659 Z= 0.115 Angle : 0.504 11.856 11760 Z= 0.256 Chirality : 0.041 0.205 1373 Planarity : 0.003 0.058 1474 Dihedral : 4.308 43.328 1269 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.38 % Allowed : 19.71 % Favored : 77.92 % 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: -0.18 (0.26), residues: 1101 helix: 1.80 (0.29), residues: 365 sheet: -0.89 (0.29), residues: 291 loop : -1.16 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 82 HIS 0.001 0.000 HIS B 142 PHE 0.022 0.001 PHE R 57 TYR 0.015 0.001 TYR D 178 ARG 0.002 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.54 seconds wall clock time: 39 minutes 10.40 seconds (2350.40 seconds total)