Starting phenix.real_space_refine on Tue Nov 14 10:37:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/11_2023/7jhj_22338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/11_2023/7jhj_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_22338/11_2023/7jhj_22338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/11_2023/7jhj_22338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/11_2023/7jhj_22338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhj_22338/11_2023/7jhj_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 4.98, per 1000 atoms: 0.59 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 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: 2.62 Time building geometry restraints manager: 3.71 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: 4388 14.08 - 28.16: 545 28.16 - 42.23: 134 42.23 - 56.31: 26 56.31 - 70.39: 5 Dihedral angle restraints: 5098 sinusoidal: 1880 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 5095 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: 0.600 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: 2.680 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- 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 : 13.449 70.389 3012 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 *********************** 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 : 1.070 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 167 average time/residue: 0.2795 time to fit residues: 59.8470 Evaluate side-chains 134 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0792 time to fit residues: 1.4864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0010 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.1469 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= 0.137 Angle : 0.494 6.114 11760 Z= 0.263 Chirality : 0.040 0.134 1373 Planarity : 0.004 0.063 1474 Dihedral : 4.928 50.948 1208 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 1.25 % Allowed : 14.16 % Favored : 84.60 % 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: -2.00 (0.24), residues: 1101 helix: -0.11 (0.27), residues: 364 sheet: -1.79 (0.27), residues: 287 loop : -1.92 (0.26), residues: 450 *********************** 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 169 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.101 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 163 average time/residue: 0.2552 time to fit residues: 54.5946 Evaluate side-chains 145 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0856 time to fit residues: 2.6473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** 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: 0.8151 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8659 Z= 0.356 Angle : 0.580 6.571 11760 Z= 0.304 Chirality : 0.044 0.151 1373 Planarity : 0.004 0.061 1474 Dihedral : 5.079 51.712 1208 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 2.15 % Allowed : 15.40 % Favored : 82.45 % 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: -1.50 (0.25), residues: 1101 helix: 0.54 (0.29), residues: 363 sheet: -1.61 (0.27), residues: 292 loop : -1.75 (0.27), residues: 446 *********************** 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 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.141 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 153 average time/residue: 0.2552 time to fit residues: 51.9484 Evaluate side-chains 137 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0908 time to fit residues: 2.5901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8659 Z= 0.141 Angle : 0.477 6.176 11760 Z= 0.251 Chirality : 0.041 0.144 1373 Planarity : 0.003 0.060 1474 Dihedral : 4.519 49.482 1208 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 1.47 % Allowed : 16.99 % Favored : 81.54 % 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: -1.01 (0.25), residues: 1101 helix: 1.04 (0.29), residues: 363 sheet: -1.41 (0.28), residues: 285 loop : -1.52 (0.27), residues: 453 *********************** 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 152 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.033 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 146 average time/residue: 0.2097 time to fit residues: 42.2646 Evaluate side-chains 134 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0883 time to fit residues: 2.1250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 331 ASN B 32 GLN B 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8659 Z= 0.347 Angle : 0.584 8.676 11760 Z= 0.300 Chirality : 0.044 0.145 1373 Planarity : 0.004 0.060 1474 Dihedral : 4.850 51.032 1208 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 1.93 % Allowed : 17.78 % Favored : 80.29 % 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: -0.97 (0.25), residues: 1101 helix: 1.04 (0.29), residues: 365 sheet: -1.42 (0.28), residues: 296 loop : -1.42 (0.28), residues: 440 *********************** 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 146 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.999 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 138 average time/residue: 0.2437 time to fit residues: 44.7998 Evaluate side-chains 137 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1363 time to fit residues: 3.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 101 optimal weight: 0.0070 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8659 Z= 0.295 Angle : 0.558 7.300 11760 Z= 0.288 Chirality : 0.043 0.142 1373 Planarity : 0.004 0.059 1474 Dihedral : 4.778 50.916 1208 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.25 % Allowed : 18.23 % Favored : 80.52 % 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: -0.82 (0.25), residues: 1101 helix: 1.16 (0.29), residues: 364 sheet: -1.32 (0.28), residues: 295 loop : -1.34 (0.28), residues: 442 *********************** 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 143 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.084 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 141 average time/residue: 0.2488 time to fit residues: 46.7514 Evaluate side-chains 135 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0838 time to fit residues: 2.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8659 Z= 0.229 Angle : 0.536 6.524 11760 Z= 0.277 Chirality : 0.042 0.149 1373 Planarity : 0.004 0.059 1474 Dihedral : 4.639 50.130 1208 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.25 % Allowed : 18.91 % Favored : 79.84 % 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: -0.64 (0.26), residues: 1101 helix: 1.35 (0.29), residues: 364 sheet: -1.29 (0.28), residues: 296 loop : -1.23 (0.29), residues: 441 *********************** 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 141 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 0.920 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 135 average time/residue: 0.2279 time to fit residues: 41.7524 Evaluate side-chains 130 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0841 time to fit residues: 1.9893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 304 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8659 Z= 0.193 Angle : 0.531 11.134 11760 Z= 0.271 Chirality : 0.042 0.146 1373 Planarity : 0.004 0.059 1474 Dihedral : 4.509 49.022 1208 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 1.13 % Allowed : 19.48 % Favored : 79.39 % 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: 1.40 (0.29), residues: 371 sheet: -1.26 (0.28), residues: 292 loop : -1.19 (0.29), residues: 438 *********************** 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 135 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.094 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 130 average time/residue: 0.2377 time to fit residues: 42.2952 Evaluate side-chains 127 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0845 time to fit residues: 2.3399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.0020 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.0370 chunk 63 optimal weight: 0.4980 overall best weight: 0.2304 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2476 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= 0.120 Angle : 0.507 11.675 11760 Z= 0.257 Chirality : 0.041 0.185 1373 Planarity : 0.003 0.059 1474 Dihedral : 4.218 45.860 1208 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 0.23 % Allowed : 19.82 % Favored : 79.95 % 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: -0.32 (0.26), residues: 1101 helix: 1.49 (0.29), residues: 377 sheet: -0.96 (0.29), residues: 291 loop : -1.13 (0.29), residues: 433 *********************** 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 138 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.032 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.2259 time to fit residues: 41.8767 Evaluate side-chains 128 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6346 time to fit residues: 2.1416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 304 GLN B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8659 Z= 0.230 Angle : 0.555 10.758 11760 Z= 0.282 Chirality : 0.043 0.179 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.390 47.501 1208 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 0.57 % Allowed : 20.05 % Favored : 79.39 % 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: 1.66 (0.29), residues: 365 sheet: -1.06 (0.29), residues: 296 loop : -1.18 (0.29), residues: 440 ********************** 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 129 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 127 average time/residue: 0.2237 time to fit residues: 38.8742 Evaluate side-chains 124 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0818 time to fit residues: 1.6416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110659 restraints weight = 11153.736| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.17 r_work: 0.3095 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8659 Z= 0.148 Angle : 0.525 11.265 11760 Z= 0.267 Chirality : 0.041 0.168 1373 Planarity : 0.003 0.059 1474 Dihedral : 4.216 45.857 1208 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 0.34 % Allowed : 20.84 % 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: -0.18 (0.26), residues: 1101 helix: 1.80 (0.29), residues: 369 sheet: -0.99 (0.29), residues: 286 loop : -1.10 (0.29), residues: 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.94 seconds wall clock time: 39 minutes 22.89 seconds (2362.89 seconds total)