Starting phenix.real_space_refine on Wed Feb 14 04:42:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/02_2024/7b03_11955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/02_2024/7b03_11955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/02_2024/7b03_11955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/02_2024/7b03_11955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/02_2024/7b03_11955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/02_2024/7b03_11955_updated.pdb" } resolution = 2.93 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.442 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 5855 2.51 5 N 1290 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E GLU 171": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "E" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 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 Time building chain proxies: 4.78, per 1000 atoms: 0.55 Number of scatterers: 8670 At special positions: 0 Unit cell: (103.2, 100.62, 67.08, 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 1470 8.00 N 1290 7.00 C 5855 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: 3.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.784A pdb=" N ARG A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 115 Proline residue: A 104 - end of helix removed outlier: 4.214A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 143 Processing helix chain 'A' and resid 149 through 168 Processing helix chain 'A' and resid 171 through 178 removed outlier: 4.111A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 198 through 208 Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'B' and resid 31 through 54 removed outlier: 3.783A pdb=" N ARG B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 115 Proline residue: B 104 - end of helix removed outlier: 4.214A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 149 through 168 Processing helix chain 'B' and resid 171 through 178 removed outlier: 4.111A pdb=" N THR B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 198 through 208 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 220 through 232 Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'C' and resid 31 through 54 removed outlier: 3.783A pdb=" N ARG C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 79 " --> pdb=" O TRP C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 115 Proline residue: C 104 - end of helix removed outlier: 4.214A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 143 Processing helix chain 'C' and resid 149 through 168 Processing helix chain 'C' and resid 171 through 178 removed outlier: 4.112A pdb=" N THR C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 Processing helix chain 'C' and resid 198 through 208 Proline residue: C 202 - end of helix Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 234 through 248 Processing helix chain 'D' and resid 31 through 54 removed outlier: 3.784A pdb=" N ARG D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 86 removed outlier: 4.343A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 79 " --> pdb=" O TRP D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 115 Proline residue: D 104 - end of helix removed outlier: 4.214A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 149 through 168 Processing helix chain 'D' and resid 171 through 178 removed outlier: 4.112A pdb=" N THR D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 Processing helix chain 'D' and resid 198 through 208 Proline residue: D 202 - end of helix Processing helix chain 'D' and resid 220 through 232 Processing helix chain 'D' and resid 234 through 248 Processing helix chain 'E' and resid 31 through 54 removed outlier: 3.783A pdb=" N ARG E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 86 removed outlier: 4.342A pdb=" N THR E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR E 79 " --> pdb=" O TRP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 115 Proline residue: E 104 - end of helix removed outlier: 4.214A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 143 Processing helix chain 'E' and resid 149 through 168 Processing helix chain 'E' and resid 171 through 178 removed outlier: 4.112A pdb=" N THR E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 198 through 208 Proline residue: E 202 - end of helix Processing helix chain 'E' and resid 220 through 232 Processing helix chain 'E' and resid 234 through 248 640 hydrogen bonds defined for protein. 1845 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: 2.55 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1288 1.32 - 1.44: 2758 1.44 - 1.57: 4789 1.57 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 8930 Sorted by residual: bond pdb=" C TRP B 75 " pdb=" O TRP B 75 " ideal model delta sigma weight residual 1.236 1.198 0.039 1.15e-02 7.56e+03 1.12e+01 bond pdb=" C TRP A 75 " pdb=" O TRP A 75 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.10e+01 bond pdb=" C TRP D 75 " pdb=" O TRP D 75 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" C TRP C 75 " pdb=" O TRP C 75 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" C TRP E 75 " pdb=" O TRP E 75 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.15e-02 7.56e+03 1.07e+01 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 91.46 - 99.96: 15 99.96 - 108.46: 338 108.46 - 116.97: 5525 116.97 - 125.47: 6077 125.47 - 133.97: 240 Bond angle restraints: 12195 Sorted by residual: angle pdb=" C16 RET D 301 " pdb=" C1 RET D 301 " pdb=" C2 RET D 301 " ideal model delta sigma weight residual 105.80 124.57 -18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C16 RET B 301 " pdb=" C1 RET B 301 " pdb=" C2 RET B 301 " ideal model delta sigma weight residual 105.80 124.55 -18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C16 RET A 301 " pdb=" C1 RET A 301 " pdb=" C2 RET A 301 " ideal model delta sigma weight residual 105.80 124.53 -18.73 3.00e+00 1.11e-01 3.90e+01 angle pdb=" C16 RET E 301 " pdb=" C1 RET E 301 " pdb=" C2 RET E 301 " ideal model delta sigma weight residual 105.80 124.51 -18.71 3.00e+00 1.11e-01 3.89e+01 angle pdb=" C16 RET C 301 " pdb=" C1 RET C 301 " pdb=" C2 RET C 301 " ideal model delta sigma weight residual 105.80 124.51 -18.71 3.00e+00 1.11e-01 3.89e+01 ... (remaining 12190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 4795 22.03 - 44.05: 115 44.05 - 66.08: 20 66.08 - 88.11: 10 88.11 - 110.13: 10 Dihedral angle restraints: 4950 sinusoidal: 1805 harmonic: 3145 Sorted by residual: dihedral pdb=" C2 RET E 301 " pdb=" C3 RET E 301 " pdb=" C4 RET E 301 " pdb=" C5 RET E 301 " ideal model delta sinusoidal sigma weight residual 42.40 -67.73 110.13 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C2 RET A 301 " pdb=" C3 RET A 301 " pdb=" C4 RET A 301 " pdb=" C5 RET A 301 " ideal model delta sinusoidal sigma weight residual 42.40 -67.71 110.11 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C2 RET D 301 " pdb=" C3 RET D 301 " pdb=" C4 RET D 301 " pdb=" C5 RET D 301 " ideal model delta sinusoidal sigma weight residual 42.40 -67.70 110.10 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 699 0.026 - 0.051: 402 0.051 - 0.077: 200 0.077 - 0.102: 50 0.102 - 0.128: 19 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CA TYR E 201 " pdb=" N TYR E 201 " pdb=" C TYR E 201 " pdb=" CB TYR E 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA TYR D 201 " pdb=" N TYR D 201 " pdb=" C TYR D 201 " pdb=" CB TYR D 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA TYR A 201 " pdb=" N TYR A 201 " pdb=" C TYR A 201 " pdb=" CB TYR A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1367 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 229 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C PHE E 229 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE E 229 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL E 230 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 229 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C PHE B 229 " -0.020 2.00e-02 2.50e+03 pdb=" O PHE B 229 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL B 230 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 229 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C PHE A 229 " -0.020 2.00e-02 2.50e+03 pdb=" O PHE A 229 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 230 " 0.007 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 548 2.73 - 3.27: 9387 3.27 - 3.82: 15420 3.82 - 4.36: 18140 4.36 - 4.90: 31031 Nonbonded interactions: 74526 Sorted by model distance: nonbonded pdb=" OH TYR E 77 " pdb=" OD2 ASP E 228 " model vdw 2.190 2.440 nonbonded pdb=" OH TYR C 77 " pdb=" OD2 ASP C 228 " model vdw 2.190 2.440 nonbonded pdb=" OH TYR B 77 " pdb=" OD2 ASP B 228 " model vdw 2.190 2.440 nonbonded pdb=" OH TYR A 77 " pdb=" OD2 ASP A 228 " model vdw 2.191 2.440 nonbonded pdb=" OH TYR D 77 " pdb=" OD2 ASP D 228 " model vdw 2.191 2.440 ... (remaining 74521 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.100 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: 1.290 Check model and map are aligned: 0.270 Set scattering table: 0.000 Process input model: 26.510 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.005 0.048 8930 Z= 0.340 Angle : 0.896 18.768 12195 Z= 0.411 Chirality : 0.039 0.128 1370 Planarity : 0.004 0.026 1450 Dihedral : 13.223 110.134 2950 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: 1.34 (0.24), residues: 1065 helix: 1.33 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 168 HIS 0.001 0.001 HIS E 76 PHE 0.012 0.002 PHE E 235 TYR 0.009 0.001 TYR E 187 ARG 0.003 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.011 Fit side-chains REVERT: A 53 ASP cc_start: 0.6808 (m-30) cc_final: 0.6579 (m-30) REVERT: A 163 MET cc_start: 0.8067 (mtp) cc_final: 0.7710 (mtp) REVERT: A 192 TYR cc_start: 0.7791 (m-80) cc_final: 0.7449 (m-80) REVERT: B 125 PHE cc_start: 0.8641 (t80) cc_final: 0.8388 (t80) REVERT: B 163 MET cc_start: 0.8195 (mtp) cc_final: 0.7972 (mtp) REVERT: B 191 MET cc_start: 0.8375 (ttm) cc_final: 0.8061 (ttp) REVERT: C 80 MET cc_start: 0.6001 (mtm) cc_final: 0.5701 (mtm) REVERT: C 147 MET cc_start: 0.6964 (ttt) cc_final: 0.6645 (ttm) REVERT: C 163 MET cc_start: 0.8090 (mtp) cc_final: 0.7610 (mtp) REVERT: C 206 PHE cc_start: 0.8079 (t80) cc_final: 0.7810 (t80) REVERT: D 141 MET cc_start: 0.8032 (mtp) cc_final: 0.7829 (ttm) REVERT: E 80 MET cc_start: 0.6062 (mtm) cc_final: 0.5771 (mtp) REVERT: E 141 MET cc_start: 0.8051 (mtp) cc_final: 0.7676 (mtm) REVERT: E 192 TYR cc_start: 0.7434 (m-80) cc_final: 0.7090 (m-80) outliers start: 0 outliers final: 1 residues processed: 209 average time/residue: 0.6192 time to fit residues: 145.6705 Evaluate side-chains 180 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 40.0000 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 219 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 241 ASN C 177 ASN C 219 ASN D 219 ASN E 219 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8930 Z= 0.244 Angle : 0.515 7.874 12195 Z= 0.263 Chirality : 0.038 0.128 1370 Planarity : 0.004 0.031 1450 Dihedral : 10.080 110.299 1217 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.84 % Allowed : 9.60 % Favored : 86.55 % 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: 1.52 (0.24), residues: 1065 helix: 1.45 (0.16), residues: 935 sheet: None (None), residues: 0 loop : -2.05 (0.39), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.013 0.002 PHE C 138 TYR 0.014 0.001 TYR B 187 ARG 0.004 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 0.893 Fit side-chains REVERT: A 34 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.6915 (t80) REVERT: A 53 ASP cc_start: 0.6871 (m-30) cc_final: 0.6530 (m-30) REVERT: A 192 TYR cc_start: 0.7836 (m-80) cc_final: 0.7566 (m-80) REVERT: B 34 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7020 (t80) REVERT: B 205 TYR cc_start: 0.7545 (t80) cc_final: 0.7333 (t80) REVERT: C 80 MET cc_start: 0.6022 (mtm) cc_final: 0.5746 (mtm) REVERT: C 147 MET cc_start: 0.6958 (ttt) cc_final: 0.6550 (ttm) REVERT: C 163 MET cc_start: 0.8124 (mtp) cc_final: 0.7663 (mtp) REVERT: C 177 ASN cc_start: 0.7813 (m-40) cc_final: 0.7366 (m-40) REVERT: C 191 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7969 (ttm) REVERT: C 192 TYR cc_start: 0.7786 (m-80) cc_final: 0.7250 (m-80) REVERT: C 206 PHE cc_start: 0.7866 (t80) cc_final: 0.7623 (t80) REVERT: C 228 ASP cc_start: 0.5807 (m-30) cc_final: 0.5482 (m-30) REVERT: D 138 PHE cc_start: 0.8486 (m-80) cc_final: 0.8226 (m-80) REVERT: D 192 TYR cc_start: 0.7488 (m-80) cc_final: 0.7093 (m-80) REVERT: E 141 MET cc_start: 0.7906 (mtp) cc_final: 0.7335 (mtm) REVERT: E 185 SER cc_start: 0.8171 (m) cc_final: 0.7961 (m) REVERT: E 191 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7947 (ttm) REVERT: E 192 TYR cc_start: 0.7380 (m-80) cc_final: 0.6995 (m-80) outliers start: 34 outliers final: 21 residues processed: 197 average time/residue: 0.6717 time to fit residues: 148.4175 Evaluate side-chains 194 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 200 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8930 Z= 0.258 Angle : 0.508 7.180 12195 Z= 0.264 Chirality : 0.038 0.129 1370 Planarity : 0.004 0.031 1450 Dihedral : 9.785 111.311 1217 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.84 % Allowed : 10.96 % Favored : 85.20 % 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: 1.38 (0.24), residues: 1065 helix: 1.35 (0.16), residues: 935 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.016 0.002 PHE C 138 TYR 0.014 0.001 TYR A 187 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.021 Fit side-chains REVERT: A 34 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6757 (t80) REVERT: A 192 TYR cc_start: 0.7766 (m-80) cc_final: 0.7508 (m-80) REVERT: B 34 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7040 (t80) REVERT: B 100 LEU cc_start: 0.8901 (tp) cc_final: 0.8615 (mt) REVERT: B 141 MET cc_start: 0.8302 (mtp) cc_final: 0.8070 (mtm) REVERT: B 191 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8298 (ttm) REVERT: C 80 MET cc_start: 0.6086 (mtm) cc_final: 0.5785 (mtm) REVERT: C 147 MET cc_start: 0.6950 (ttt) cc_final: 0.6533 (ttm) REVERT: C 163 MET cc_start: 0.8270 (mtp) cc_final: 0.7941 (mtp) REVERT: C 177 ASN cc_start: 0.7779 (m-40) cc_final: 0.7272 (m-40) REVERT: C 191 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7934 (ttm) REVERT: C 192 TYR cc_start: 0.7694 (m-80) cc_final: 0.7261 (m-80) REVERT: C 206 PHE cc_start: 0.7856 (t80) cc_final: 0.7603 (t80) REVERT: D 192 TYR cc_start: 0.7470 (m-80) cc_final: 0.7143 (m-80) REVERT: E 138 PHE cc_start: 0.8348 (m-80) cc_final: 0.8146 (OUTLIER) REVERT: E 141 MET cc_start: 0.7886 (mtp) cc_final: 0.7586 (ttm) REVERT: E 185 SER cc_start: 0.8203 (m) cc_final: 0.7979 (m) REVERT: E 191 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7919 (ttm) REVERT: E 192 TYR cc_start: 0.7380 (m-80) cc_final: 0.7005 (m-80) REVERT: E 220 LEU cc_start: 0.8232 (tp) cc_final: 0.8006 (tp) outliers start: 34 outliers final: 26 residues processed: 193 average time/residue: 0.6347 time to fit residues: 137.3795 Evaluate side-chains 203 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 200 ILE 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: 5.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8930 Z= 0.183 Angle : 0.459 6.773 12195 Z= 0.238 Chirality : 0.036 0.124 1370 Planarity : 0.003 0.028 1450 Dihedral : 9.567 111.759 1217 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.95 % Allowed : 12.88 % Favored : 83.16 % 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: 1.63 (0.24), residues: 1065 helix: 1.52 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.001 HIS C 76 PHE 0.012 0.001 PHE B 138 TYR 0.014 0.001 TYR A 187 ARG 0.004 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 0.897 Fit side-chains REVERT: A 34 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6764 (t80) REVERT: A 192 TYR cc_start: 0.7757 (m-80) cc_final: 0.7481 (m-80) REVERT: B 34 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7039 (t80) REVERT: B 100 LEU cc_start: 0.8828 (tp) cc_final: 0.8515 (mt) REVERT: B 141 MET cc_start: 0.8250 (mtp) cc_final: 0.8046 (mtm) REVERT: B 191 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8139 (ttm) REVERT: C 80 MET cc_start: 0.6073 (mtm) cc_final: 0.5809 (mtm) REVERT: C 147 MET cc_start: 0.6800 (ttt) cc_final: 0.6360 (ttm) REVERT: C 163 MET cc_start: 0.8075 (mtp) cc_final: 0.7705 (mtp) REVERT: C 177 ASN cc_start: 0.7760 (m-40) cc_final: 0.7253 (m-40) REVERT: C 192 TYR cc_start: 0.7691 (m-80) cc_final: 0.7342 (m-80) REVERT: C 206 PHE cc_start: 0.7810 (t80) cc_final: 0.7565 (t80) REVERT: C 228 ASP cc_start: 0.5733 (m-30) cc_final: 0.5373 (m-30) REVERT: D 192 TYR cc_start: 0.7475 (m-80) cc_final: 0.7206 (m-80) REVERT: E 34 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.6966 (t80) REVERT: E 141 MET cc_start: 0.7815 (mtp) cc_final: 0.7534 (ttm) REVERT: E 185 SER cc_start: 0.8154 (m) cc_final: 0.7946 (m) REVERT: E 191 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7736 (ttm) REVERT: E 192 TYR cc_start: 0.7350 (m-80) cc_final: 0.7021 (m-80) outliers start: 35 outliers final: 21 residues processed: 198 average time/residue: 0.6386 time to fit residues: 141.6506 Evaluate side-chains 207 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8930 Z= 0.291 Angle : 0.540 6.829 12195 Z= 0.277 Chirality : 0.038 0.131 1370 Planarity : 0.004 0.032 1450 Dihedral : 9.484 109.087 1215 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.52 % Allowed : 14.69 % Favored : 80.79 % 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: 1.28 (0.24), residues: 1065 helix: 1.28 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 84 HIS 0.004 0.002 HIS D 76 PHE 0.015 0.002 PHE B 138 TYR 0.018 0.002 TYR A 187 ARG 0.004 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 0.941 Fit side-chains REVERT: A 34 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 192 TYR cc_start: 0.7802 (m-80) cc_final: 0.7542 (m-80) REVERT: B 34 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7030 (t80) REVERT: B 100 LEU cc_start: 0.8913 (tp) cc_final: 0.8633 (mt) REVERT: B 191 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8289 (ttm) REVERT: C 80 MET cc_start: 0.5843 (mtm) cc_final: 0.5554 (mtm) REVERT: C 147 MET cc_start: 0.6845 (ttt) cc_final: 0.6390 (ttm) REVERT: C 163 MET cc_start: 0.8313 (mtp) cc_final: 0.7882 (mtp) REVERT: C 191 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7956 (ttm) REVERT: C 192 TYR cc_start: 0.7714 (m-80) cc_final: 0.7327 (m-80) REVERT: C 206 PHE cc_start: 0.7823 (t80) cc_final: 0.7586 (t80) REVERT: E 141 MET cc_start: 0.7956 (mtp) cc_final: 0.7662 (ttm) REVERT: E 185 SER cc_start: 0.8214 (m) cc_final: 0.7988 (m) REVERT: E 191 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7937 (ttm) REVERT: E 192 TYR cc_start: 0.7382 (m-80) cc_final: 0.7027 (m-80) outliers start: 40 outliers final: 26 residues processed: 201 average time/residue: 0.6354 time to fit residues: 143.7610 Evaluate side-chains 206 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 84 optimal weight: 40.0000 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8930 Z= 0.241 Angle : 0.510 7.893 12195 Z= 0.261 Chirality : 0.037 0.127 1370 Planarity : 0.003 0.030 1450 Dihedral : 9.359 111.484 1215 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.52 % Allowed : 15.71 % Favored : 79.77 % 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: 1.35 (0.24), residues: 1065 helix: 1.35 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -2.00 (0.41), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 84 HIS 0.003 0.002 HIS D 76 PHE 0.015 0.002 PHE B 138 TYR 0.017 0.001 TYR A 187 ARG 0.004 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 0.857 Fit side-chains REVERT: A 34 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6748 (t80) REVERT: A 192 TYR cc_start: 0.7792 (m-80) cc_final: 0.7520 (m-80) REVERT: B 34 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7016 (t80) REVERT: B 100 LEU cc_start: 0.8885 (tp) cc_final: 0.8587 (mt) REVERT: B 191 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8156 (ttm) REVERT: C 80 MET cc_start: 0.5831 (mtm) cc_final: 0.5533 (mtm) REVERT: C 147 MET cc_start: 0.6846 (ttt) cc_final: 0.6416 (ttm) REVERT: C 191 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7847 (ttm) REVERT: C 192 TYR cc_start: 0.7699 (m-80) cc_final: 0.7362 (m-80) REVERT: C 206 PHE cc_start: 0.7797 (t80) cc_final: 0.7580 (t80) REVERT: E 34 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.6912 (t80) REVERT: E 141 MET cc_start: 0.7935 (mtp) cc_final: 0.7630 (ttm) REVERT: E 185 SER cc_start: 0.8205 (m) cc_final: 0.7976 (m) REVERT: E 191 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7841 (ttm) REVERT: E 192 TYR cc_start: 0.7365 (m-80) cc_final: 0.6964 (m-80) outliers start: 40 outliers final: 25 residues processed: 200 average time/residue: 0.6262 time to fit residues: 140.0653 Evaluate side-chains 209 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 63 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8930 Z= 0.213 Angle : 0.496 8.526 12195 Z= 0.254 Chirality : 0.037 0.126 1370 Planarity : 0.003 0.029 1450 Dihedral : 9.019 111.019 1215 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.95 % Allowed : 16.84 % Favored : 79.21 % 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: 1.46 (0.24), residues: 1065 helix: 1.43 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.016 0.002 PHE D 206 TYR 0.016 0.001 TYR A 187 ARG 0.004 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 0.985 Fit side-chains REVERT: A 34 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 58 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7776 (ptmt) REVERT: A 192 TYR cc_start: 0.7786 (m-80) cc_final: 0.7510 (m-80) REVERT: B 34 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6996 (t80) REVERT: B 100 LEU cc_start: 0.8846 (tp) cc_final: 0.8536 (mt) REVERT: B 191 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8105 (ttm) REVERT: C 80 MET cc_start: 0.5815 (mtm) cc_final: 0.5539 (mtm) REVERT: C 147 MET cc_start: 0.6841 (ttt) cc_final: 0.6414 (ttm) REVERT: C 191 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7766 (ttm) REVERT: C 192 TYR cc_start: 0.7697 (m-80) cc_final: 0.7394 (m-80) REVERT: C 206 PHE cc_start: 0.7787 (t80) cc_final: 0.7558 (t80) REVERT: E 34 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6999 (t80) REVERT: E 141 MET cc_start: 0.7891 (mtp) cc_final: 0.7610 (ttm) REVERT: E 185 SER cc_start: 0.8343 (m) cc_final: 0.8103 (m) REVERT: E 191 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7763 (ttm) REVERT: E 192 TYR cc_start: 0.7358 (m-80) cc_final: 0.6975 (m-80) outliers start: 35 outliers final: 24 residues processed: 209 average time/residue: 0.6188 time to fit residues: 145.3131 Evaluate side-chains 214 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8930 Z= 0.226 Angle : 0.501 9.201 12195 Z= 0.259 Chirality : 0.037 0.127 1370 Planarity : 0.003 0.029 1450 Dihedral : 8.497 110.638 1215 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.73 % Allowed : 17.29 % Favored : 78.98 % 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: 1.41 (0.24), residues: 1065 helix: 1.39 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.97 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.016 0.002 PHE E 206 TYR 0.016 0.001 TYR A 187 ARG 0.004 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.099 Fit side-chains REVERT: A 34 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6766 (t80) REVERT: A 58 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7753 (ptmt) REVERT: A 141 MET cc_start: 0.7945 (mtp) cc_final: 0.7487 (mtp) REVERT: A 192 TYR cc_start: 0.7786 (m-80) cc_final: 0.7501 (m-80) REVERT: B 34 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6958 (t80) REVERT: B 100 LEU cc_start: 0.8867 (tp) cc_final: 0.8552 (mt) REVERT: B 132 SER cc_start: 0.8422 (p) cc_final: 0.8114 (p) REVERT: B 191 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: C 80 MET cc_start: 0.5820 (mtm) cc_final: 0.5543 (mtm) REVERT: C 147 MET cc_start: 0.6840 (ttt) cc_final: 0.6400 (ttm) REVERT: C 191 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7969 (ttm) REVERT: C 192 TYR cc_start: 0.7677 (m-80) cc_final: 0.7351 (m-80) REVERT: E 34 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.6940 (t80) REVERT: E 141 MET cc_start: 0.7920 (mtp) cc_final: 0.7588 (ttm) REVERT: E 185 SER cc_start: 0.8346 (m) cc_final: 0.8109 (m) REVERT: E 191 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7862 (ttm) REVERT: E 192 TYR cc_start: 0.7360 (m-80) cc_final: 0.6971 (m-80) outliers start: 33 outliers final: 23 residues processed: 198 average time/residue: 0.6614 time to fit residues: 146.6500 Evaluate side-chains 210 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8930 Z= 0.190 Angle : 0.480 10.827 12195 Z= 0.249 Chirality : 0.036 0.130 1370 Planarity : 0.003 0.028 1450 Dihedral : 8.513 110.331 1215 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.62 % Allowed : 17.97 % Favored : 78.42 % 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: 1.58 (0.24), residues: 1065 helix: 1.51 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.94 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.014 0.001 PHE D 206 TYR 0.016 0.001 TYR A 187 ARG 0.003 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.051 Fit side-chains REVERT: A 34 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6762 (t80) REVERT: A 58 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7714 (ptmt) REVERT: A 141 MET cc_start: 0.7902 (mtp) cc_final: 0.7452 (mtp) REVERT: A 192 TYR cc_start: 0.7777 (m-80) cc_final: 0.7491 (m-80) REVERT: B 34 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6946 (t80) REVERT: B 100 LEU cc_start: 0.8833 (tp) cc_final: 0.8517 (mt) REVERT: B 132 SER cc_start: 0.8408 (p) cc_final: 0.8059 (p) REVERT: B 191 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8132 (ttm) REVERT: C 80 MET cc_start: 0.5813 (mtm) cc_final: 0.5542 (mtm) REVERT: C 147 MET cc_start: 0.6790 (ttt) cc_final: 0.6380 (ttm) REVERT: C 191 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7774 (ttm) REVERT: C 192 TYR cc_start: 0.7664 (m-80) cc_final: 0.7345 (m-80) REVERT: E 34 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7001 (t80) REVERT: E 141 MET cc_start: 0.7892 (mtp) cc_final: 0.7546 (ttm) REVERT: E 185 SER cc_start: 0.8328 (m) cc_final: 0.8095 (m) REVERT: E 191 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7645 (ttm) REVERT: E 192 TYR cc_start: 0.7349 (m-80) cc_final: 0.6987 (m-80) outliers start: 32 outliers final: 23 residues processed: 199 average time/residue: 0.6397 time to fit residues: 142.3256 Evaluate side-chains 208 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 0.0040 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8930 Z= 0.156 Angle : 0.450 9.815 12195 Z= 0.237 Chirality : 0.036 0.129 1370 Planarity : 0.003 0.027 1450 Dihedral : 8.599 109.571 1215 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.73 % Allowed : 17.85 % Favored : 78.42 % 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: 1.85 (0.24), residues: 1065 helix: 1.70 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.90 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.003 0.002 HIS B 76 PHE 0.019 0.001 PHE E 206 TYR 0.014 0.001 TYR A 187 ARG 0.003 0.000 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 0.975 Fit side-chains REVERT: A 34 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6877 (t80) REVERT: A 141 MET cc_start: 0.7861 (mtp) cc_final: 0.7456 (mtp) REVERT: A 192 TYR cc_start: 0.7765 (m-80) cc_final: 0.7490 (m-80) REVERT: B 34 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6986 (t80) REVERT: B 75 TRP cc_start: 0.8530 (t-100) cc_final: 0.8043 (t60) REVERT: B 191 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8107 (ttm) REVERT: C 80 MET cc_start: 0.5811 (mtm) cc_final: 0.5510 (mtm) REVERT: C 147 MET cc_start: 0.6746 (ttt) cc_final: 0.6326 (ttm) REVERT: C 191 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7756 (ttm) REVERT: C 192 TYR cc_start: 0.7664 (m-80) cc_final: 0.7385 (m-80) REVERT: C 228 ASP cc_start: 0.5561 (m-30) cc_final: 0.5256 (m-30) REVERT: E 34 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7000 (t80) REVERT: E 141 MET cc_start: 0.7840 (mtp) cc_final: 0.7492 (ttm) REVERT: E 185 SER cc_start: 0.8334 (m) cc_final: 0.8095 (m) REVERT: E 191 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7675 (ttm) REVERT: E 192 TYR cc_start: 0.7346 (m-80) cc_final: 0.7000 (m-80) outliers start: 33 outliers final: 25 residues processed: 203 average time/residue: 0.6247 time to fit residues: 142.2317 Evaluate side-chains 212 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.161766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.137284 restraints weight = 9190.760| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.21 r_work: 0.3278 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8930 Z= 0.168 Angle : 0.465 9.822 12195 Z= 0.243 Chirality : 0.036 0.128 1370 Planarity : 0.003 0.027 1450 Dihedral : 8.495 107.876 1215 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.73 % Allowed : 17.97 % Favored : 78.31 % 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: 1.90 (0.24), residues: 1065 helix: 1.72 (0.16), residues: 925 sheet: None (None), residues: 0 loop : -1.85 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 35 HIS 0.003 0.002 HIS D 76 PHE 0.019 0.001 PHE E 206 TYR 0.014 0.001 TYR A 187 ARG 0.003 0.001 ARG E 52 =============================================================================== Job complete usr+sys time: 2711.74 seconds wall clock time: 49 minutes 25.64 seconds (2965.64 seconds total)