Starting phenix.real_space_refine on Mon Mar 11 06:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/03_2024/7sfj_25079_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/03_2024/7sfj_25079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/03_2024/7sfj_25079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/03_2024/7sfj_25079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/03_2024/7sfj_25079_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/03_2024/7sfj_25079_updated.pdb" } resolution = 2.74 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= 0.003 sd= 0.175 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 4983 2.51 5 N 1098 2.21 5 O 1245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 272": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7377 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PEE': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 6, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 159 Unusual residues: {'PEE': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 5, 'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 150 Unusual residues: {'PEE': 6, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 4, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.64 Number of scatterers: 7377 At special positions: 0 Unit cell: (78.453, 77.316, 88.686, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 1245 8.00 N 1098 7.00 C 4983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 0 sheets defined 69.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 27 through 52 Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 69 through 94 removed outlier: 4.476A pdb=" N ALA A 74 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 199 Processing helix chain 'A' and resid 206 through 232 removed outlier: 3.899A pdb=" N HIS A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TRP A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 225 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 245 through 269 removed outlier: 3.884A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.739A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 27 through 52 Processing helix chain 'B' and resid 64 through 67 No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 69 through 94 removed outlier: 4.476A pdb=" N ALA B 74 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY B 87 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 137 through 157 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 165 through 199 Processing helix chain 'B' and resid 206 through 232 removed outlier: 3.900A pdb=" N HIS B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 225 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 245 through 269 removed outlier: 3.884A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.739A pdb=" N GLY B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N HIS B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 27 through 52 Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 69 through 94 removed outlier: 4.476A pdb=" N ALA C 74 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Proline residue: C 121 - end of helix Processing helix chain 'C' and resid 137 through 157 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 165 through 199 Processing helix chain 'C' and resid 206 through 232 removed outlier: 3.900A pdb=" N HIS C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU C 225 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 245 through 269 removed outlier: 3.883A pdb=" N CYS C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.739A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2079 1.34 - 1.46: 1569 1.46 - 1.57: 3858 1.57 - 1.69: 3 1.69 - 1.81: 75 Bond restraints: 7584 Sorted by residual: bond pdb=" C30 PEE B 403 " pdb=" O5 PEE B 403 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C30 PEE A 403 " pdb=" O5 PEE A 403 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C10 PEE A 401 " pdb=" O4 PEE A 401 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C10 PEE C 403 " pdb=" O4 PEE C 403 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C30 PEE C 405 " pdb=" O5 PEE C 405 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.32e+01 ... (remaining 7579 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.79: 108 105.79 - 112.85: 3875 112.85 - 119.92: 2639 119.92 - 126.99: 3424 126.99 - 134.06: 133 Bond angle restraints: 10179 Sorted by residual: angle pdb=" C11 PEE C 403 " pdb=" C10 PEE C 403 " pdb=" O2 PEE C 403 " ideal model delta sigma weight residual 111.70 123.90 -12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 123.87 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C11 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 111.70 123.86 -12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C31 PEE B 403 " pdb=" C30 PEE B 403 " pdb=" O3 PEE B 403 " ideal model delta sigma weight residual 111.87 123.93 -12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C31 PEE A 403 " pdb=" C30 PEE A 403 " pdb=" O3 PEE A 403 " ideal model delta sigma weight residual 111.87 123.88 -12.01 3.00e+00 1.11e-01 1.60e+01 ... (remaining 10174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 4127 30.46 - 60.91: 175 60.91 - 91.37: 12 91.37 - 121.83: 9 121.83 - 152.28: 9 Dihedral angle restraints: 4332 sinusoidal: 1857 harmonic: 2475 Sorted by residual: dihedral pdb=" C32 PEE B 406 " pdb=" C30 PEE B 406 " pdb=" C31 PEE B 406 " pdb=" O3 PEE B 406 " ideal model delta sinusoidal sigma weight residual 161.16 8.88 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C32 PEE A 407 " pdb=" C30 PEE A 407 " pdb=" C31 PEE A 407 " pdb=" O3 PEE A 407 " ideal model delta sinusoidal sigma weight residual 161.16 8.88 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C32 PEE C 401 " pdb=" C30 PEE C 401 " pdb=" C31 PEE C 401 " pdb=" O3 PEE C 401 " ideal model delta sinusoidal sigma weight residual 161.16 8.93 152.23 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 707 0.037 - 0.074: 237 0.074 - 0.111: 52 0.111 - 0.147: 12 0.147 - 0.184: 3 Chirality restraints: 1011 Sorted by residual: chirality pdb=" CB ILE B 224 " pdb=" CA ILE B 224 " pdb=" CG1 ILE B 224 " pdb=" CG2 ILE B 224 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB ILE A 224 " pdb=" CA ILE A 224 " pdb=" CG1 ILE A 224 " pdb=" CG2 ILE A 224 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CB ILE C 224 " pdb=" CA ILE C 224 " pdb=" CG1 ILE C 224 " pdb=" CG2 ILE C 224 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 1008 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 233 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 234 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 233 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 234 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 233 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 234 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.026 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2284 2.83 - 3.34: 6897 3.34 - 3.86: 11960 3.86 - 4.38: 14377 4.38 - 4.90: 24659 Nonbonded interactions: 60177 Sorted by model distance: nonbonded pdb=" NH1 ARG A 195 " pdb=" O LEU A 282 " model vdw 2.308 2.520 nonbonded pdb=" NH1 ARG C 195 " pdb=" O LEU C 282 " model vdw 2.308 2.520 nonbonded pdb=" NH1 ARG B 195 " pdb=" O LEU B 282 " model vdw 2.308 2.520 nonbonded pdb=" OG SER B 51 " pdb=" OD1 ASN B 72 " model vdw 2.314 2.440 nonbonded pdb=" OG SER A 51 " pdb=" OD1 ASN A 72 " model vdw 2.314 2.440 ... (remaining 60172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ e C39 or name C40 or name C41 or name C42)))) selection = (chain 'B' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ e C39 or name C40 or name C41 or name C42)))) selection = (chain 'C' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ e C39 or name C40 or name C41 or name C42)))) } 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: 0.530 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: 2.630 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.730 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.007 0.147 7584 Z= 0.438 Angle : 0.940 12.201 10179 Z= 0.400 Chirality : 0.040 0.184 1011 Planarity : 0.005 0.047 1242 Dihedral : 18.487 152.281 2766 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.28 % Allowed : 1.28 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.28), residues: 843 helix: 1.78 (0.21), residues: 579 sheet: None (None), residues: 0 loop : 0.95 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 177 HIS 0.003 0.001 HIS B 33 PHE 0.010 0.001 PHE A 173 TYR 0.012 0.001 TYR A 271 ARG 0.003 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: B 122 MET cc_start: 0.8558 (mtt) cc_final: 0.8328 (mtm) REVERT: C 117 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8300 (ttm) outliers start: 9 outliers final: 0 residues processed: 90 average time/residue: 1.4059 time to fit residues: 133.0451 Evaluate side-chains 63 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS B 243 ASN C 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7584 Z= 0.232 Angle : 0.510 4.933 10179 Z= 0.264 Chirality : 0.039 0.126 1011 Planarity : 0.005 0.046 1242 Dihedral : 15.660 117.932 1314 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.28 % Allowed : 8.26 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.29), residues: 843 helix: 1.84 (0.22), residues: 579 sheet: None (None), residues: 0 loop : 1.17 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 19 HIS 0.003 0.001 HIS C 33 PHE 0.018 0.002 PHE B 173 TYR 0.021 0.002 TYR B 271 ARG 0.003 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.715 Fit side-chains REVERT: A 68 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6464 (mm-40) REVERT: A 277 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.5723 (mpt-90) REVERT: B 68 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6526 (mt0) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 1.5557 time to fit residues: 104.4581 Evaluate side-chains 64 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.0010 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7584 Z= 0.151 Angle : 0.438 5.058 10179 Z= 0.228 Chirality : 0.037 0.121 1011 Planarity : 0.004 0.045 1242 Dihedral : 13.431 110.201 1311 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.99 % Allowed : 11.11 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.30), residues: 843 helix: 2.10 (0.22), residues: 579 sheet: None (None), residues: 0 loop : 1.14 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 PHE 0.011 0.001 PHE A 173 TYR 0.014 0.001 TYR C 271 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.740 Fit side-chains REVERT: A 68 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6501 (mm-40) REVERT: A 277 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.5697 (mpt-90) outliers start: 14 outliers final: 4 residues processed: 65 average time/residue: 1.7050 time to fit residues: 115.8609 Evaluate side-chains 64 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 269 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN B 165 ASN C 78 ASN C 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7584 Z= 0.205 Angle : 0.469 4.823 10179 Z= 0.246 Chirality : 0.038 0.130 1011 Planarity : 0.004 0.046 1242 Dihedral : 13.455 111.234 1311 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.14 % Allowed : 11.82 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.29), residues: 843 helix: 2.02 (0.22), residues: 579 sheet: None (None), residues: 0 loop : 1.12 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 19 HIS 0.003 0.001 HIS A 96 PHE 0.014 0.001 PHE B 173 TYR 0.019 0.001 TYR C 271 ARG 0.002 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.777 Fit side-chains REVERT: A 68 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6489 (mm-40) REVERT: A 277 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.5516 (mpt-90) REVERT: B 10 MET cc_start: 0.7948 (mtm) cc_final: 0.7627 (mtp) REVERT: B 68 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6730 (mt0) outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 1.6259 time to fit residues: 109.1290 Evaluate side-chains 69 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7584 Z= 0.142 Angle : 0.423 4.802 10179 Z= 0.221 Chirality : 0.036 0.121 1011 Planarity : 0.004 0.045 1242 Dihedral : 12.530 110.396 1311 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.71 % Allowed : 13.11 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.29), residues: 843 helix: 2.12 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 1.18 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 19 HIS 0.002 0.001 HIS A 96 PHE 0.011 0.001 PHE B 173 TYR 0.013 0.001 TYR C 271 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.799 Fit side-chains REVERT: A 68 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6480 (mm-40) REVERT: A 277 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5726 (mpt-90) REVERT: B 68 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6617 (mt0) REVERT: B 164 ARG cc_start: 0.6348 (tmt170) cc_final: 0.6067 (tmt170) outliers start: 12 outliers final: 6 residues processed: 64 average time/residue: 1.6777 time to fit residues: 112.4452 Evaluate side-chains 65 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7584 Z= 0.170 Angle : 0.442 4.800 10179 Z= 0.231 Chirality : 0.037 0.123 1011 Planarity : 0.004 0.045 1242 Dihedral : 12.644 111.062 1311 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.28 % Allowed : 13.68 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.29), residues: 843 helix: 2.07 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 1.14 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 19 HIS 0.003 0.001 HIS B 96 PHE 0.013 0.001 PHE C 173 TYR 0.016 0.001 TYR C 271 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.870 Fit side-chains REVERT: A 68 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6630 (mm-40) REVERT: A 277 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.5722 (mpt-90) REVERT: B 10 MET cc_start: 0.7836 (mtm) cc_final: 0.7533 (mtp) REVERT: B 68 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6609 (mt0) outliers start: 16 outliers final: 8 residues processed: 67 average time/residue: 1.6458 time to fit residues: 115.4403 Evaluate side-chains 69 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 165 ASN B 78 ASN C 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7584 Z= 0.257 Angle : 0.499 4.909 10179 Z= 0.261 Chirality : 0.039 0.125 1011 Planarity : 0.004 0.047 1242 Dihedral : 13.400 111.601 1311 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.56 % Allowed : 13.68 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.29), residues: 843 helix: 1.90 (0.22), residues: 579 sheet: None (None), residues: 0 loop : 0.99 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 19 HIS 0.004 0.001 HIS C 96 PHE 0.015 0.001 PHE C 173 TYR 0.023 0.002 TYR C 271 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.750 Fit side-chains REVERT: A 68 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6621 (mm-40) REVERT: A 277 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.5632 (mpt-90) REVERT: B 10 MET cc_start: 0.7941 (mtm) cc_final: 0.7606 (mtp) REVERT: B 68 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7101 (mm-40) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 1.4648 time to fit residues: 110.7147 Evaluate side-chains 70 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 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 165 ASN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7584 Z= 0.222 Angle : 0.476 4.887 10179 Z= 0.248 Chirality : 0.038 0.121 1011 Planarity : 0.004 0.047 1242 Dihedral : 13.188 111.403 1311 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.85 % Allowed : 13.39 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.29), residues: 843 helix: 1.86 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 1.05 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 19 HIS 0.003 0.001 HIS C 96 PHE 0.014 0.001 PHE C 173 TYR 0.020 0.001 TYR C 271 ARG 0.003 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.614 Fit side-chains REVERT: A 68 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6626 (mm-40) REVERT: A 277 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5506 (mpt-90) REVERT: B 10 MET cc_start: 0.7937 (mtm) cc_final: 0.7598 (mtp) REVERT: B 68 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7062 (mm-40) REVERT: B 152 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7411 (mm) outliers start: 20 outliers final: 12 residues processed: 71 average time/residue: 1.5788 time to fit residues: 117.3021 Evaluate side-chains 74 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7584 Z= 0.324 Angle : 0.546 4.975 10179 Z= 0.284 Chirality : 0.041 0.178 1011 Planarity : 0.005 0.050 1242 Dihedral : 14.093 113.181 1311 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.85 % Allowed : 13.68 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.29), residues: 843 helix: 1.67 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.90 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 19 HIS 0.004 0.001 HIS A 96 PHE 0.016 0.002 PHE B 173 TYR 0.028 0.002 TYR C 271 ARG 0.003 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6651 (mm-40) REVERT: A 164 ARG cc_start: 0.7129 (ttm170) cc_final: 0.6353 (tpt170) REVERT: A 277 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5683 (mpt-90) REVERT: B 10 MET cc_start: 0.7972 (mtm) cc_final: 0.7637 (mtp) REVERT: B 68 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7128 (mm-40) REVERT: B 152 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7502 (mm) REVERT: B 164 ARG cc_start: 0.6432 (tmt170) cc_final: 0.6093 (tmt170) REVERT: C 68 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7286 (mp10) outliers start: 20 outliers final: 13 residues processed: 71 average time/residue: 1.5885 time to fit residues: 118.1431 Evaluate side-chains 76 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 165 ASN B 78 ASN B 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7584 Z= 0.153 Angle : 0.446 4.801 10179 Z= 0.231 Chirality : 0.037 0.190 1011 Planarity : 0.004 0.048 1242 Dihedral : 12.865 111.094 1311 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.42 % Allowed : 13.96 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.29), residues: 843 helix: 1.91 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.99 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 19 HIS 0.003 0.001 HIS B 96 PHE 0.012 0.001 PHE C 173 TYR 0.014 0.001 TYR C 271 ARG 0.003 0.000 ARG B 164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6548 (mm-40) REVERT: A 164 ARG cc_start: 0.7002 (ttm170) cc_final: 0.6288 (tpt170) REVERT: A 277 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5702 (mpt-90) REVERT: B 10 MET cc_start: 0.7938 (mtm) cc_final: 0.7614 (mtp) REVERT: B 68 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6953 (mm-40) REVERT: B 152 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7286 (mm) REVERT: B 164 ARG cc_start: 0.6462 (tmt170) cc_final: 0.6173 (tmt170) REVERT: C 68 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7197 (mp10) outliers start: 17 outliers final: 12 residues processed: 70 average time/residue: 1.6158 time to fit residues: 118.5478 Evaluate side-chains 76 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.0070 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114219 restraints weight = 8245.305| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.89 r_work: 0.3365 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7584 Z= 0.141 Angle : 0.434 4.847 10179 Z= 0.225 Chirality : 0.037 0.185 1011 Planarity : 0.004 0.046 1242 Dihedral : 12.405 109.834 1311 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.14 % Allowed : 14.25 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.30), residues: 843 helix: 1.99 (0.22), residues: 585 sheet: None (None), residues: 0 loop : 1.02 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 19 HIS 0.003 0.001 HIS B 96 PHE 0.011 0.001 PHE C 173 TYR 0.012 0.001 TYR C 271 ARG 0.002 0.000 ARG B 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.35 seconds wall clock time: 45 minutes 32.23 seconds (2732.23 seconds total)