Starting phenix.real_space_refine on Fri Jul 19 11:42:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/07_2024/7sfj_25079.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/07_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_25079/07_2024/7sfj_25079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/07_2024/7sfj_25079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/07_2024/7sfj_25079.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfj_25079/07_2024/7sfj_25079.cif" } 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-5388/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: 4.77, per 1000 atoms: 0.65 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 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... Secondary structure from input PDB file: 39 helices and 3 sheets defined 74.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 26 through 53 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.597A pdb=" N TYR A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.515A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.748A pdb=" N THR A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 164 through 200 removed outlier: 3.936A pdb=" N TYR A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.711A pdb=" N LEU A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 244 through 268 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 272 through 283 removed outlier: 3.739A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 26 through 53 Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.596A pdb=" N TYR B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.515A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.749A pdb=" N THR B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 136 through 158 Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 164 through 200 removed outlier: 3.936A pdb=" N TYR B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.710A pdb=" N LEU B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 244 through 268 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 272 through 283 removed outlier: 3.739A pdb=" N GLY B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 53 Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.596A pdb=" N TYR C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 95 removed outlier: 3.515A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 removed outlier: 3.748A pdb=" N THR C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Proline residue: C 121 - end of helix Processing helix chain 'C' and resid 136 through 158 Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 164 through 200 removed outlier: 3.935A pdb=" N TYR C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.711A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 244 through 268 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 272 through 283 removed outlier: 3.739A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 4.573A pdb=" N ALA A 4 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4 removed outlier: 4.572A pdb=" N ALA B 4 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 7 " --> pdb=" O ALA B 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 4.572A pdb=" N ALA C 4 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 7 " --> pdb=" O ALA C 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 444 hydrogen bonds defined for protein. 1305 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: 1.80 Time building geometry restraints manager: 2.99 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: 2269 2.83 - 3.34: 6885 3.34 - 3.86: 12038 3.86 - 4.38: 14221 4.38 - 4.90: 24644 Nonbonded interactions: 60057 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 60052 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: 0.600 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.310 Find NCS groups from input model: 0.440 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- 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= 0.491 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 : 0.757 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: 1.4176 time to fit residues: 134.1453 Evaluate side-chains 63 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS C 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1593 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= 0.245 Angle : 0.514 4.986 10179 Z= 0.267 Chirality : 0.039 0.126 1011 Planarity : 0.004 0.046 1242 Dihedral : 16.035 124.234 1314 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.42 % Allowed : 8.26 % Favored : 90.31 % 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: 2.93 (0.29), residues: 843 helix: 2.36 (0.22), residues: 585 sheet: None (None), residues: 0 loop : 1.10 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 19 HIS 0.003 0.001 HIS C 3 PHE 0.017 0.002 PHE B 173 TYR 0.019 0.002 TYR C 271 ARG 0.002 0.000 ARG B 235 *********************** 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 73 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.747 Fit side-chains REVERT: A 68 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6443 (mm-40) REVERT: A 260 TYR cc_start: 0.7780 (t80) cc_final: 0.7288 (t80) REVERT: B 68 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6617 (mt0) REVERT: C 277 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.5456 (mpt-90) outliers start: 10 outliers final: 2 residues processed: 65 average time/residue: 1.7550 time to fit residues: 119.6153 Evaluate side-chains 62 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 277 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.1875 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= 0.148 Angle : 0.430 5.033 10179 Z= 0.223 Chirality : 0.037 0.121 1011 Planarity : 0.003 0.044 1242 Dihedral : 13.241 110.104 1311 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.85 % Allowed : 10.97 % Favored : 87.18 % 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: 3.31 (0.29), residues: 843 helix: 2.70 (0.22), residues: 585 sheet: None (None), residues: 0 loop : 1.10 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 19 HIS 0.002 0.001 HIS C 3 PHE 0.011 0.001 PHE C 173 TYR 0.012 0.001 TYR B 271 ARG 0.002 0.000 ARG B 277 *********************** 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: 13 poor density : 62 time to evaluate : 0.738 Fit side-chains REVERT: A 68 GLN cc_start: 0.6796 (mt0) cc_final: 0.6396 (mm-40) REVERT: B 164 ARG cc_start: 0.6697 (ttm-80) cc_final: 0.6155 (tmt170) REVERT: B 277 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6992 (mmt90) REVERT: C 68 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6757 (mm-40) outliers start: 13 outliers final: 2 residues processed: 67 average time/residue: 1.7445 time to fit residues: 121.9496 Evaluate side-chains 64 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 68 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 81 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 C 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7584 Z= 0.365 Angle : 0.575 4.948 10179 Z= 0.299 Chirality : 0.043 0.136 1011 Planarity : 0.004 0.049 1242 Dihedral : 14.784 113.613 1311 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.42 % Allowed : 12.68 % Favored : 84.90 % 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: 2.71 (0.29), residues: 843 helix: 2.22 (0.22), residues: 588 sheet: None (None), residues: 0 loop : 0.95 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 19 HIS 0.005 0.001 HIS A 96 PHE 0.018 0.002 PHE B 173 TYR 0.031 0.002 TYR C 271 ARG 0.003 0.001 ARG B 235 *********************** 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 81 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.728 Fit side-chains REVERT: A 68 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6732 (mm-40) REVERT: A 260 TYR cc_start: 0.7814 (t80) cc_final: 0.7337 (t80) REVERT: A 277 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.5896 (mpt-90) REVERT: B 10 MET cc_start: 0.8020 (mtm) cc_final: 0.7680 (mtp) REVERT: B 269 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7738 (mttm) REVERT: B 277 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.7005 (mtt-85) REVERT: C 68 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6878 (mm-40) REVERT: C 260 TYR cc_start: 0.8069 (t80) cc_final: 0.7844 (t80) REVERT: C 277 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.5605 (mpt-90) outliers start: 17 outliers final: 6 residues processed: 71 average time/residue: 1.5784 time to fit residues: 117.3446 Evaluate side-chains 72 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 277 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7584 Z= 0.242 Angle : 0.490 4.710 10179 Z= 0.255 Chirality : 0.039 0.128 1011 Planarity : 0.004 0.049 1242 Dihedral : 13.849 112.586 1311 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.99 % Allowed : 13.25 % 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: 2.80 (0.29), residues: 843 helix: 2.37 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.78 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 19 HIS 0.003 0.001 HIS C 96 PHE 0.014 0.001 PHE A 173 TYR 0.019 0.001 TYR C 271 ARG 0.003 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 79 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.844 Fit side-chains REVERT: A 68 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6516 (mm-40) REVERT: A 260 TYR cc_start: 0.7702 (t80) cc_final: 0.7258 (t80) REVERT: B 10 MET cc_start: 0.8014 (mtm) cc_final: 0.7675 (mtp) REVERT: B 269 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7696 (mttm) REVERT: B 277 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6933 (mtt-85) outliers start: 21 outliers final: 7 residues processed: 70 average time/residue: 1.6387 time to fit residues: 119.9312 Evaluate side-chains 65 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 271 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7584 Z= 0.249 Angle : 0.498 4.714 10179 Z= 0.259 Chirality : 0.039 0.128 1011 Planarity : 0.004 0.049 1242 Dihedral : 13.857 112.989 1311 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.71 % Allowed : 13.96 % Favored : 83.33 % 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: 2.79 (0.29), residues: 843 helix: 2.33 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.82 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 19 HIS 0.003 0.001 HIS C 96 PHE 0.015 0.001 PHE B 173 TYR 0.019 0.002 TYR C 271 ARG 0.003 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 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.741 Fit side-chains REVERT: A 68 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6431 (mm-40) REVERT: A 260 TYR cc_start: 0.7688 (t80) cc_final: 0.7410 (t80) REVERT: B 10 MET cc_start: 0.8041 (mtm) cc_final: 0.7685 (mtp) REVERT: B 152 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7530 (mm) REVERT: B 277 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6847 (mtt-85) REVERT: C 260 TYR cc_start: 0.8045 (t80) cc_final: 0.7785 (t80) outliers start: 19 outliers final: 8 residues processed: 72 average time/residue: 1.6193 time to fit residues: 122.2014 Evaluate side-chains 69 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 271 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7584 Z= 0.167 Angle : 0.447 4.610 10179 Z= 0.231 Chirality : 0.037 0.123 1011 Planarity : 0.004 0.047 1242 Dihedral : 12.984 112.803 1311 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.71 % Allowed : 14.53 % Favored : 82.76 % 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: 3.02 (0.29), residues: 843 helix: 2.54 (0.22), residues: 588 sheet: None (None), residues: 0 loop : 0.82 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 PHE 0.011 0.001 PHE C 173 TYR 0.013 0.001 TYR C 271 ARG 0.002 0.000 ARG C 277 *********************** 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 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.807 Fit side-chains REVERT: A 68 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6372 (mm-40) REVERT: A 269 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7602 (mttm) REVERT: B 10 MET cc_start: 0.7993 (mtm) cc_final: 0.7647 (mtp) REVERT: B 152 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7480 (mm) REVERT: B 164 ARG cc_start: 0.6852 (ttm-80) cc_final: 0.6251 (tmt170) REVERT: B 277 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6841 (mtt-85) outliers start: 19 outliers final: 7 residues processed: 76 average time/residue: 1.5823 time to fit residues: 125.9055 Evaluate side-chains 70 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 138 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.0000 chunk 70 optimal weight: 2.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2578 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= 0.192 Angle : 0.470 5.268 10179 Z= 0.241 Chirality : 0.039 0.210 1011 Planarity : 0.004 0.047 1242 Dihedral : 13.065 112.938 1311 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.99 % Allowed : 14.39 % Favored : 82.62 % 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: 3.02 (0.29), residues: 843 helix: 2.54 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.79 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 19 HIS 0.002 0.001 HIS C 96 PHE 0.012 0.001 PHE C 173 TYR 0.014 0.001 TYR C 271 ARG 0.002 0.000 ARG C 277 *********************** 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 78 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.769 Fit side-chains REVERT: A 68 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6398 (mm-40) REVERT: A 269 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7610 (mttm) REVERT: B 10 MET cc_start: 0.8010 (mtm) cc_final: 0.7667 (mtp) REVERT: B 152 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7544 (mm) REVERT: B 277 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6830 (mtt-85) REVERT: C 68 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7103 (mp10) outliers start: 21 outliers final: 10 residues processed: 71 average time/residue: 1.6063 time to fit residues: 119.7716 Evaluate side-chains 71 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 277 ARG 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 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: 0.0570 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7584 Z= 0.168 Angle : 0.456 5.172 10179 Z= 0.233 Chirality : 0.038 0.217 1011 Planarity : 0.004 0.046 1242 Dihedral : 12.751 112.806 1311 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.99 % Allowed : 14.10 % Favored : 82.91 % 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: 3.09 (0.29), residues: 843 helix: 2.64 (0.22), residues: 585 sheet: None (None), residues: 0 loop : 0.71 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 19 HIS 0.002 0.001 HIS C 96 PHE 0.011 0.001 PHE C 173 TYR 0.012 0.001 TYR B 271 ARG 0.002 0.000 ARG C 277 *********************** 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: 21 poor density : 59 time to evaluate : 0.687 Fit side-chains REVERT: A 68 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6405 (mm-40) REVERT: A 164 ARG cc_start: 0.6992 (ttm170) cc_final: 0.6155 (tpt170) REVERT: A 269 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7597 (mttm) REVERT: B 10 MET cc_start: 0.8004 (mtm) cc_final: 0.7659 (mtp) REVERT: B 152 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7538 (mm) REVERT: B 164 ARG cc_start: 0.6789 (ttm-80) cc_final: 0.6207 (tmt170) REVERT: B 277 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6810 (mtt-85) REVERT: C 68 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7181 (mp10) outliers start: 21 outliers final: 11 residues processed: 72 average time/residue: 1.5128 time to fit residues: 114.1957 Evaluate side-chains 74 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 277 ARG 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 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: 0.0980 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7584 Z= 0.111 Angle : 0.415 5.285 10179 Z= 0.212 Chirality : 0.036 0.217 1011 Planarity : 0.003 0.045 1242 Dihedral : 12.108 112.256 1311 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.14 % Allowed : 15.81 % Favored : 83.05 % 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: 3.29 (0.29), residues: 843 helix: 2.82 (0.22), residues: 585 sheet: None (None), residues: 0 loop : 0.73 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 19 HIS 0.002 0.000 HIS B 96 PHE 0.010 0.001 PHE C 173 TYR 0.008 0.001 TYR C 193 ARG 0.002 0.000 ARG B 277 ********************** 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 71 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.661 Fit side-chains REVERT: A 68 GLN cc_start: 0.6688 (mt0) cc_final: 0.6304 (mm-40) REVERT: A 164 ARG cc_start: 0.6796 (ttm170) cc_final: 0.6021 (tpt170) REVERT: B 10 MET cc_start: 0.7982 (mtm) cc_final: 0.7650 (mtp) REVERT: B 152 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7432 (mm) REVERT: B 164 ARG cc_start: 0.6824 (ttm-80) cc_final: 0.6176 (tmt170) REVERT: B 277 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6757 (mtt180) REVERT: C 68 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6973 (mp10) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 1.5361 time to fit residues: 111.0283 Evaluate side-chains 66 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.0170 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117205 restraints weight = 8239.334| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.97 r_work: 0.3403 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7584 Z= 0.109 Angle : 0.410 5.598 10179 Z= 0.209 Chirality : 0.037 0.232 1011 Planarity : 0.003 0.044 1242 Dihedral : 11.910 111.912 1311 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.85 % Allowed : 16.24 % Favored : 82.91 % 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: 3.37 (0.30), residues: 843 helix: 2.87 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.77 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 177 HIS 0.002 0.000 HIS B 96 PHE 0.010 0.001 PHE C 173 TYR 0.008 0.001 TYR B 168 ARG 0.004 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2531.05 seconds wall clock time: 45 minutes 32.52 seconds (2732.52 seconds total)