Starting phenix.real_space_refine on Sat Aug 3 16:08:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqc_16795/08_2024/8cqc_16795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqc_16795/08_2024/8cqc_16795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqc_16795/08_2024/8cqc_16795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqc_16795/08_2024/8cqc_16795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqc_16795/08_2024/8cqc_16795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqc_16795/08_2024/8cqc_16795.cif" } resolution = 2.82 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= 0.019 sd= 0.276 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5880 2.51 5 N 1300 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8735 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "B" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "C" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "D" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "E" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 9.35, per 1000 atoms: 1.07 Number of scatterers: 8735 At special positions: 0 Unit cell: (102.479, 101.475, 67.3149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1500 8.00 N 1300 7.00 C 5880 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 2.8 seconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 90.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 30 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 56 through 87 removed outlier: 4.605A pdb=" N THR A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 118 removed outlier: 3.516A pdb=" N TRP A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 4.245A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 144 Processing helix chain 'A' and resid 148 through 169 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 220 through 249 removed outlier: 4.169A pdb=" N PHE A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 56 through 87 removed outlier: 4.603A pdb=" N THR B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 118 removed outlier: 3.509A pdb=" N TRP B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 4.262A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 148 through 169 Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 220 through 249 removed outlier: 4.166A pdb=" N PHE B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 51 Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 56 through 87 removed outlier: 4.604A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 118 removed outlier: 3.511A pdb=" N TRP C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 4.242A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 144 Processing helix chain 'C' and resid 148 through 169 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 220 through 249 removed outlier: 4.156A pdb=" N PHE C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 56 through 87 removed outlier: 4.602A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 118 removed outlier: 3.510A pdb=" N TRP D 99 " --> pdb=" O ARG D 95 " (cutoff:3.500A) Proline residue: D 104 - end of helix removed outlier: 4.229A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 144 Processing helix chain 'D' and resid 148 through 169 Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 220 through 249 removed outlier: 4.160A pdb=" N PHE D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 51 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 56 through 87 removed outlier: 4.603A pdb=" N THR E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 118 removed outlier: 3.511A pdb=" N TRP E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Proline residue: E 104 - end of helix removed outlier: 4.278A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 Processing helix chain 'E' and resid 148 through 169 Processing helix chain 'E' and resid 170 through 177 Processing helix chain 'E' and resid 180 through 197 Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 220 through 249 removed outlier: 4.137A pdb=" N PHE E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1270 1.29 - 1.42: 2685 1.42 - 1.55: 4910 1.55 - 1.68: 15 1.68 - 1.81: 95 Bond restraints: 8975 Sorted by residual: bond pdb=" C ARG A 95 " pdb=" O ARG A 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.27e+01 bond pdb=" C ARG B 95 " pdb=" O ARG B 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.27e+01 bond pdb=" C ARG C 95 " pdb=" O ARG C 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.26e+01 bond pdb=" C ARG E 95 " pdb=" O ARG E 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.26e+01 bond pdb=" C ARG D 95 " pdb=" O ARG D 95 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.31e-02 5.83e+03 3.22e+01 ... (remaining 8970 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 210 106.76 - 113.57: 4830 113.57 - 120.38: 3519 120.38 - 127.19: 3561 127.19 - 133.99: 145 Bond angle restraints: 12265 Sorted by residual: angle pdb=" N ARG E 95 " pdb=" CA ARG E 95 " pdb=" C ARG E 95 " ideal model delta sigma weight residual 113.18 106.53 6.65 1.21e+00 6.83e-01 3.02e+01 angle pdb=" N ARG C 95 " pdb=" CA ARG C 95 " pdb=" C ARG C 95 " ideal model delta sigma weight residual 113.18 106.56 6.62 1.21e+00 6.83e-01 2.99e+01 angle pdb=" N ARG D 95 " pdb=" CA ARG D 95 " pdb=" C ARG D 95 " ideal model delta sigma weight residual 113.18 106.57 6.61 1.21e+00 6.83e-01 2.99e+01 angle pdb=" N ARG A 95 " pdb=" CA ARG A 95 " pdb=" C ARG A 95 " ideal model delta sigma weight residual 113.18 106.58 6.60 1.21e+00 6.83e-01 2.98e+01 angle pdb=" N ARG B 95 " pdb=" CA ARG B 95 " pdb=" C ARG B 95 " ideal model delta sigma weight residual 113.18 106.60 6.58 1.21e+00 6.83e-01 2.96e+01 ... (remaining 12260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4694 17.18 - 34.36: 241 34.36 - 51.53: 35 51.53 - 68.71: 0 68.71 - 85.89: 10 Dihedral angle restraints: 4980 sinusoidal: 1815 harmonic: 3165 Sorted by residual: dihedral pdb=" CB GLU D 246 " pdb=" CG GLU D 246 " pdb=" CD GLU D 246 " pdb=" OE1 GLU D 246 " ideal model delta sinusoidal sigma weight residual 0.00 85.89 -85.89 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CB GLU B 246 " pdb=" CG GLU B 246 " pdb=" CD GLU B 246 " pdb=" OE1 GLU B 246 " ideal model delta sinusoidal sigma weight residual 0.00 84.31 -84.31 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" CB GLU A 246 " pdb=" CG GLU A 246 " pdb=" CD GLU A 246 " pdb=" OE1 GLU A 246 " ideal model delta sinusoidal sigma weight residual 0.00 83.42 -83.42 1 3.00e+01 1.11e-03 9.44e+00 ... (remaining 4977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 806 0.027 - 0.053: 355 0.053 - 0.080: 127 0.080 - 0.107: 60 0.107 - 0.133: 27 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA ILE D 72 " pdb=" N ILE D 72 " pdb=" C ILE D 72 " pdb=" CB ILE D 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 72 " pdb=" N ILE B 72 " pdb=" C ILE B 72 " pdb=" CB ILE B 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1372 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 75 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C TRP C 75 " 0.049 2.00e-02 2.50e+03 pdb=" O TRP C 75 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS C 76 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 75 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C TRP D 75 " -0.049 2.00e-02 2.50e+03 pdb=" O TRP D 75 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS D 76 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 75 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C TRP A 75 " -0.049 2.00e-02 2.50e+03 pdb=" O TRP A 75 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 76 " 0.016 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3783 2.91 - 3.40: 9706 3.40 - 3.90: 15388 3.90 - 4.40: 17813 4.40 - 4.90: 29433 Nonbonded interactions: 76123 Sorted by model distance: nonbonded pdb=" O LYS E 58 " pdb=" O HOH E 401 " model vdw 2.406 3.040 nonbonded pdb=" O LYS B 58 " pdb=" O HOH B 401 " model vdw 2.408 3.040 nonbonded pdb=" O LYS A 58 " pdb=" O HOH A 401 " model vdw 2.408 3.040 nonbonded pdb=" O LYS C 58 " pdb=" O HOH C 401 " model vdw 2.408 3.040 nonbonded pdb=" O LYS D 58 " pdb=" O HOH D 401 " model vdw 2.408 3.040 ... (remaining 76118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 75 or resid 77 through 249 or resid 301)) selection = (chain 'B' and (resid 25 through 75 or resid 77 through 249 or resid 301)) selection = (chain 'C' and (resid 25 through 75 or resid 77 through 249 or resid 301)) selection = (chain 'D' and (resid 25 through 75 or resid 77 through 249 or resid 301)) selection = (chain 'E' and (resid 25 through 75 or resid 77 through 249 or resid 301)) } 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=0.50 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 32.850 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.006 0.075 8975 Z= 0.379 Angle : 0.718 6.653 12265 Z= 0.476 Chirality : 0.039 0.133 1375 Planarity : 0.004 0.034 1460 Dihedral : 10.914 85.888 2970 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.34 % Allowed : 3.48 % Favored : 96.18 % 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: 0.69 (0.25), residues: 1070 helix: 0.73 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.13 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 75 PHE 0.014 0.002 PHE A 235 TYR 0.015 0.002 TYR B 205 ARG 0.003 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7778 (mtmm) REVERT: A 192 TYR cc_start: 0.7804 (m-80) cc_final: 0.7520 (m-80) REVERT: B 192 TYR cc_start: 0.7882 (m-80) cc_final: 0.7304 (m-80) REVERT: C 53 ASP cc_start: 0.7751 (m-30) cc_final: 0.7447 (m-30) REVERT: C 190 MET cc_start: 0.8570 (mtp) cc_final: 0.8328 (mtm) REVERT: C 192 TYR cc_start: 0.7854 (m-80) cc_final: 0.7199 (m-80) REVERT: E 58 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7883 (mtmm) REVERT: E 192 TYR cc_start: 0.7981 (m-80) cc_final: 0.7368 (m-80) outliers start: 3 outliers final: 3 residues processed: 115 average time/residue: 0.9921 time to fit residues: 123.4274 Evaluate side-chains 101 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 184 GLN D 184 GLN D 231 ASN ** E 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8975 Z= 0.199 Angle : 0.513 8.872 12265 Z= 0.280 Chirality : 0.038 0.126 1375 Planarity : 0.004 0.033 1460 Dihedral : 4.205 40.530 1231 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.90 % Allowed : 8.54 % Favored : 90.56 % 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: 2.17 (0.25), residues: 1070 helix: 1.76 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.16 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 75 PHE 0.014 0.002 PHE D 235 TYR 0.020 0.001 TYR E 77 ARG 0.003 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7539 (t80) cc_final: 0.7323 (t80) REVERT: A 166 GLU cc_start: 0.7282 (tp30) cc_final: 0.6893 (mm-30) REVERT: A 192 TYR cc_start: 0.7712 (m-80) cc_final: 0.7477 (m-80) REVERT: B 192 TYR cc_start: 0.7896 (m-80) cc_final: 0.7315 (m-80) REVERT: C 190 MET cc_start: 0.8491 (mtp) cc_final: 0.8244 (mtm) REVERT: C 192 TYR cc_start: 0.7823 (m-80) cc_final: 0.7201 (m-80) REVERT: E 58 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7682 (mtmm) REVERT: E 166 GLU cc_start: 0.7282 (tp30) cc_final: 0.7066 (tp30) REVERT: E 192 TYR cc_start: 0.7920 (m-80) cc_final: 0.7353 (m-80) outliers start: 8 outliers final: 4 residues processed: 115 average time/residue: 0.9991 time to fit residues: 124.9306 Evaluate side-chains 107 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 95 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 184 GLN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN ** E 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8975 Z= 0.210 Angle : 0.537 12.251 12265 Z= 0.283 Chirality : 0.038 0.113 1375 Planarity : 0.004 0.034 1460 Dihedral : 4.008 42.131 1227 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.35 % Allowed : 8.54 % Favored : 90.11 % 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: 2.29 (0.25), residues: 1070 helix: 1.82 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.95 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 75 PHE 0.013 0.002 PHE C 235 TYR 0.011 0.001 TYR B 79 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7713 (m-80) cc_final: 0.7488 (m-80) REVERT: B 192 TYR cc_start: 0.7857 (m-80) cc_final: 0.7291 (m-80) REVERT: C 190 MET cc_start: 0.8504 (mtp) cc_final: 0.8292 (mtm) REVERT: C 192 TYR cc_start: 0.7830 (m-80) cc_final: 0.7226 (m-80) REVERT: D 147 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6682 (tpp) REVERT: E 58 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7625 (mtmm) REVERT: E 192 TYR cc_start: 0.7916 (m-80) cc_final: 0.7345 (m-80) outliers start: 12 outliers final: 7 residues processed: 117 average time/residue: 0.9301 time to fit residues: 118.1937 Evaluate side-chains 103 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.0970 chunk 27 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 231 ASN ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 231 ASN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8975 Z= 0.148 Angle : 0.469 9.673 12265 Z= 0.248 Chirality : 0.036 0.107 1375 Planarity : 0.003 0.032 1460 Dihedral : 3.806 39.773 1227 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.56 % Allowed : 9.78 % Favored : 89.66 % 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: 2.56 (0.25), residues: 1070 helix: 2.01 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.90 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 75 PHE 0.011 0.001 PHE D 235 TYR 0.008 0.001 TYR B 79 ARG 0.002 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7667 (m-80) cc_final: 0.7261 (m-80) REVERT: B 192 TYR cc_start: 0.7803 (m-80) cc_final: 0.7217 (m-80) REVERT: C 192 TYR cc_start: 0.7715 (m-80) cc_final: 0.7073 (m-80) REVERT: E 192 TYR cc_start: 0.7854 (m-80) cc_final: 0.7298 (m-80) outliers start: 5 outliers final: 4 residues processed: 110 average time/residue: 0.9516 time to fit residues: 113.7874 Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8975 Z= 0.185 Angle : 0.477 4.933 12265 Z= 0.257 Chirality : 0.037 0.111 1375 Planarity : 0.003 0.033 1460 Dihedral : 3.848 38.367 1227 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 10.34 % Favored : 88.31 % 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: 2.54 (0.25), residues: 1070 helix: 2.00 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.93 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 75 PHE 0.013 0.002 PHE E 235 TYR 0.008 0.001 TYR D 187 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7687 (m-80) cc_final: 0.7326 (m-80) REVERT: B 192 TYR cc_start: 0.7780 (m-80) cc_final: 0.7277 (m-80) REVERT: C 192 TYR cc_start: 0.7691 (m-80) cc_final: 0.7093 (m-80) REVERT: E 192 TYR cc_start: 0.7859 (m-80) cc_final: 0.7313 (m-80) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 0.9807 time to fit residues: 114.8762 Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8975 Z= 0.159 Angle : 0.475 8.457 12265 Z= 0.253 Chirality : 0.037 0.108 1375 Planarity : 0.003 0.032 1460 Dihedral : 3.788 37.117 1227 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.90 % Allowed : 10.56 % Favored : 88.54 % 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 (0.25), residues: 1070 helix: 2.04 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.95 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 75 PHE 0.013 0.001 PHE D 235 TYR 0.019 0.001 TYR A 79 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7671 (m-80) cc_final: 0.7264 (m-80) REVERT: B 192 TYR cc_start: 0.7704 (m-80) cc_final: 0.7159 (m-80) REVERT: C 192 TYR cc_start: 0.7653 (m-80) cc_final: 0.7033 (m-80) REVERT: E 192 TYR cc_start: 0.7841 (m-80) cc_final: 0.7303 (m-80) outliers start: 6 outliers final: 5 residues processed: 107 average time/residue: 0.9722 time to fit residues: 112.9836 Evaluate side-chains 103 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 76 HIS B ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8975 Z= 0.220 Angle : 0.508 7.751 12265 Z= 0.271 Chirality : 0.038 0.116 1375 Planarity : 0.004 0.033 1460 Dihedral : 3.925 37.016 1227 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.35 % Allowed : 10.34 % Favored : 88.31 % 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: 2.46 (0.24), residues: 1070 helix: 1.95 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.05 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 75 PHE 0.014 0.002 PHE A 235 TYR 0.019 0.001 TYR A 79 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7735 (m-80) cc_final: 0.7421 (m-80) REVERT: B 192 TYR cc_start: 0.7839 (m-80) cc_final: 0.7274 (m-80) REVERT: C 192 TYR cc_start: 0.7700 (m-80) cc_final: 0.7089 (m-80) REVERT: D 147 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6802 (ttt) REVERT: E 192 TYR cc_start: 0.7892 (m-80) cc_final: 0.7355 (m-80) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 1.0356 time to fit residues: 119.7404 Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8975 Z= 0.168 Angle : 0.478 7.192 12265 Z= 0.254 Chirality : 0.037 0.109 1375 Planarity : 0.003 0.032 1460 Dihedral : 3.855 37.059 1227 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.24 % Allowed : 10.56 % Favored : 88.20 % 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: 2.58 (0.24), residues: 1070 helix: 2.03 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.07 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 75 PHE 0.013 0.001 PHE D 235 TYR 0.017 0.001 TYR A 79 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7714 (m-80) cc_final: 0.7345 (m-80) REVERT: B 192 TYR cc_start: 0.7668 (m-80) cc_final: 0.7139 (m-80) REVERT: C 192 TYR cc_start: 0.7672 (m-80) cc_final: 0.7066 (m-80) REVERT: D 147 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6791 (ttt) REVERT: E 192 TYR cc_start: 0.7855 (m-80) cc_final: 0.7315 (m-80) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 1.0684 time to fit residues: 117.5523 Evaluate side-chains 100 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8975 Z= 0.168 Angle : 0.476 5.149 12265 Z= 0.254 Chirality : 0.037 0.109 1375 Planarity : 0.003 0.032 1460 Dihedral : 3.844 36.858 1227 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.01 % Allowed : 11.01 % Favored : 87.98 % 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 (0.24), residues: 1070 helix: 2.07 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.05 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 75 PHE 0.013 0.001 PHE D 235 TYR 0.017 0.001 TYR A 79 ARG 0.002 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7714 (m-80) cc_final: 0.7288 (m-80) REVERT: B 192 TYR cc_start: 0.7648 (m-80) cc_final: 0.7130 (m-80) REVERT: C 192 TYR cc_start: 0.7667 (m-80) cc_final: 0.7059 (m-80) REVERT: D 147 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6803 (ttt) REVERT: E 192 TYR cc_start: 0.7849 (m-80) cc_final: 0.7311 (m-80) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 1.0950 time to fit residues: 115.8841 Evaluate side-chains 98 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN ** E 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8975 Z= 0.169 Angle : 0.495 11.203 12265 Z= 0.261 Chirality : 0.037 0.108 1375 Planarity : 0.003 0.032 1460 Dihedral : 3.854 36.894 1227 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.90 % Allowed : 10.90 % Favored : 88.20 % 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 (0.24), residues: 1070 helix: 2.07 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.05 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 75 PHE 0.013 0.001 PHE D 235 TYR 0.016 0.001 TYR C 79 ARG 0.002 0.000 ARG C 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7709 (m-80) cc_final: 0.7287 (m-80) REVERT: B 192 TYR cc_start: 0.7646 (m-80) cc_final: 0.7130 (m-80) REVERT: C 192 TYR cc_start: 0.7666 (m-80) cc_final: 0.7057 (m-80) REVERT: D 147 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6819 (ttt) REVERT: E 192 TYR cc_start: 0.7841 (m-80) cc_final: 0.7326 (m-80) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 1.1133 time to fit residues: 117.6420 Evaluate side-chains 99 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8025 > 50: distance: 70 - 89: 7.398 distance: 75 - 96: 9.973 distance: 78 - 82: 3.107 distance: 79 - 102: 5.830 distance: 82 - 83: 3.541 distance: 83 - 84: 6.832 distance: 83 - 86: 4.435 distance: 84 - 89: 5.068 distance: 85 - 106: 21.858 distance: 86 - 87: 8.090 distance: 86 - 88: 8.702 distance: 89 - 90: 4.030 distance: 90 - 91: 3.273 distance: 90 - 93: 3.925 distance: 91 - 92: 7.109 distance: 91 - 96: 5.740 distance: 92 - 114: 18.431 distance: 93 - 94: 4.189 distance: 96 - 97: 5.101 distance: 97 - 98: 4.792 distance: 97 - 100: 10.809 distance: 98 - 99: 5.377 distance: 98 - 102: 5.653 distance: 99 - 121: 30.269 distance: 100 - 101: 4.989 distance: 103 - 104: 15.543 distance: 104 - 105: 7.587 distance: 104 - 106: 8.716 distance: 105 - 128: 35.066 distance: 107 - 108: 5.520 distance: 107 - 110: 8.942 distance: 109 - 132: 14.838 distance: 111 - 113: 16.875 distance: 114 - 115: 6.186 distance: 115 - 116: 10.199 distance: 115 - 118: 28.033 distance: 116 - 117: 8.653 distance: 116 - 121: 34.077 distance: 117 - 140: 11.723 distance: 118 - 119: 12.257 distance: 118 - 120: 22.683 distance: 121 - 122: 35.218 distance: 122 - 123: 16.150 distance: 122 - 125: 27.838 distance: 123 - 124: 5.731 distance: 123 - 128: 8.936 distance: 124 - 145: 12.729 distance: 125 - 126: 19.406 distance: 128 - 129: 11.401 distance: 129 - 130: 9.345 distance: 130 - 131: 5.597 distance: 130 - 132: 5.938 distance: 131 - 152: 19.273 distance: 132 - 133: 6.699 distance: 133 - 134: 5.641 distance: 133 - 136: 9.021 distance: 134 - 135: 6.982 distance: 134 - 140: 4.225 distance: 135 - 158: 6.550 distance: 136 - 137: 10.911 distance: 136 - 138: 8.718 distance: 137 - 139: 13.828 distance: 140 - 141: 11.932 distance: 141 - 144: 14.017 distance: 142 - 143: 7.399 distance: 143 - 172: 6.065