Starting phenix.real_space_refine on Sun Mar 17 02:29:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/03_2024/8d1g_27129_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/03_2024/8d1g_27129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/03_2024/8d1g_27129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/03_2024/8d1g_27129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/03_2024/8d1g_27129_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/03_2024/8d1g_27129_trim.pdb" } resolution = 2.07 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= -0.002 sd= 0.130 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 80 5.16 5 Cl 1 4.86 5 C 10490 2.51 5 N 2355 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 303": "OD1" <-> "OD2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 303": "OD1" <-> "OD2" Residue "D GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16201 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "B" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "E" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "C" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "D" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 247 Unusual residues: {' CA': 1, ' CL': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Time building chain proxies: 16.38, per 1000 atoms: 1.01 Number of scatterers: 16201 At special positions: 0 Unit cell: (90.47, 92.13, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 80 16.00 P 15 15.00 O 3255 8.00 N 2355 7.00 C 10490 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=0, symmetry=0 Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 4.5 seconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.593A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 296 removed outlier: 4.497A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.607A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 296 removed outlier: 4.497A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 980 hydrogen bonds defined for protein. 2830 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: 3.86 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2240 1.32 - 1.44: 4570 1.44 - 1.56: 8985 1.56 - 1.69: 30 1.69 - 1.81: 120 Bond restraints: 15945 Sorted by residual: bond pdb=" N VAL D 81 " pdb=" CA VAL D 81 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.18e+00 bond pdb=" N VAL C 81 " pdb=" CA VAL C 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.90e+00 bond pdb=" N VAL A 81 " pdb=" CA VAL A 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.86e+00 bond pdb=" N VAL B 81 " pdb=" CA VAL B 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.83e+00 bond pdb=" N VAL E 81 " pdb=" CA VAL E 81 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.58e+00 ... (remaining 15940 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.75: 250 105.75 - 112.85: 7971 112.85 - 119.94: 6207 119.94 - 127.04: 6791 127.04 - 134.13: 156 Bond angle restraints: 21375 Sorted by residual: angle pdb=" O3P MC3 E 505 " pdb=" P MC3 E 505 " pdb=" O4P MC3 E 505 " ideal model delta sigma weight residual 93.26 104.22 -10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 A 504 " pdb=" P MC3 A 504 " pdb=" O4P MC3 A 504 " ideal model delta sigma weight residual 93.26 104.22 -10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 B 504 " pdb=" P MC3 B 504 " pdb=" O4P MC3 B 504 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 C 504 " pdb=" P MC3 C 504 " pdb=" O4P MC3 C 504 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 D 505 " pdb=" P MC3 D 505 " pdb=" O4P MC3 D 505 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 ... (remaining 21370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 8848 27.46 - 54.91: 807 54.91 - 82.37: 140 82.37 - 109.83: 30 109.83 - 137.28: 10 Dihedral angle restraints: 9835 sinusoidal: 4685 harmonic: 5150 Sorted by residual: dihedral pdb=" C33 MC3 D 505 " pdb=" C31 MC3 D 505 " pdb=" C32 MC3 D 505 " pdb=" O2 MC3 D 505 " ideal model delta sinusoidal sigma weight residual 175.52 -47.20 -137.28 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C33 MC3 C 504 " pdb=" C31 MC3 C 504 " pdb=" C32 MC3 C 504 " pdb=" O2 MC3 C 504 " ideal model delta sinusoidal sigma weight residual 175.52 -47.20 -137.28 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C33 MC3 A 504 " pdb=" C31 MC3 A 504 " pdb=" C32 MC3 A 504 " pdb=" O2 MC3 A 504 " ideal model delta sinusoidal sigma weight residual 175.52 -47.22 -137.26 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 9832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1453 0.034 - 0.067: 590 0.067 - 0.101: 141 0.101 - 0.135: 46 0.135 - 0.168: 15 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CA VAL B 232 " pdb=" N VAL B 232 " pdb=" C VAL B 232 " pdb=" CB VAL B 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA VAL D 232 " pdb=" N VAL D 232 " pdb=" C VAL D 232 " pdb=" CB VAL D 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA VAL A 232 " pdb=" N VAL A 232 " pdb=" C VAL A 232 " pdb=" CB VAL A 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 2242 not shown) Planarity restraints: 2530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 282 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C PHE E 282 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE E 282 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE E 283 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 282 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C PHE D 282 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE D 282 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE D 283 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 282 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C PHE B 282 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE B 282 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE B 283 " -0.009 2.00e-02 2.50e+03 ... (remaining 2527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1879 2.75 - 3.28: 16364 3.28 - 3.82: 31540 3.82 - 4.36: 38590 4.36 - 4.90: 60758 Nonbonded interactions: 149131 Sorted by model distance: nonbonded pdb=" O HOH B 655 " pdb=" O HOH C 704 " model vdw 2.207 2.440 nonbonded pdb=" O HOH A 704 " pdb=" O HOH E 655 " model vdw 2.215 2.440 nonbonded pdb=" O HOH A 655 " pdb=" O HOH B 704 " model vdw 2.215 2.440 nonbonded pdb=" O HOH E 704 " pdb=" O HOH D 656 " model vdw 2.219 2.440 nonbonded pdb=" O HOH C 655 " pdb=" O HOH D 704 " model vdw 2.226 2.440 ... (remaining 149126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'B' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'C' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'D' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 or (resid 505 through 506 and (name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C40 or name C41 or name C42 or name C43 or name C44)) or (resid 507 through 5 \ 08 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid \ 509 or (resid 510 and (name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name \ C44)) or (resid 511 through 512 and (name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'E' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 or (resid 505 through 506 and (name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C40 or name C41 or name C42 or name C43 or name C44)) or (resid 507 through 5 \ 08 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid \ 509 or (resid 510 and (name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name \ C44)) or (resid 511 through 512 and (name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44)))) } 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: 4.250 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: 0.020 Extract box with map and model: 14.070 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 52.510 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 0.050 15945 Z= 0.376 Angle : 0.690 10.959 21375 Z= 0.368 Chirality : 0.041 0.168 2245 Planarity : 0.003 0.018 2530 Dihedral : 20.598 137.282 6535 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.66 % Allowed : 12.46 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1715 helix: 1.80 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.14 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 338 HIS 0.004 0.001 HIS D 115 PHE 0.020 0.002 PHE E 248 TYR 0.024 0.002 TYR B 97 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 1.818 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7231 (ptp90) cc_final: 0.6794 (mtt180) REVERT: E 13 ARG cc_start: 0.7072 (ptp90) cc_final: 0.6777 (mpt180) REVERT: C 13 ARG cc_start: 0.7230 (ptp90) cc_final: 0.6845 (mpt180) REVERT: C 159 GLU cc_start: 0.7370 (mp0) cc_final: 0.6981 (mm-30) REVERT: D 13 ARG cc_start: 0.7324 (ptp90) cc_final: 0.6928 (mtt90) REVERT: D 44 MET cc_start: 0.8753 (mmt) cc_final: 0.8448 (mmm) REVERT: D 71 GLN cc_start: 0.7831 (tt0) cc_final: 0.7630 (tt0) REVERT: D 333 GLU cc_start: 0.7205 (tt0) cc_final: 0.6901 (pm20) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 1.6383 time to fit residues: 388.4126 Evaluate side-chains 179 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 303 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 316 GLN B 19 GLN B 173 ASN B 175 ASN B 316 GLN E 173 ASN E 175 ASN E 316 GLN C 175 ASN C 316 GLN D 19 GLN D 316 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15945 Z= 0.191 Angle : 0.538 5.904 21375 Z= 0.294 Chirality : 0.038 0.164 2245 Planarity : 0.004 0.025 2530 Dihedral : 17.534 115.617 3273 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.18 % Allowed : 10.30 % Favored : 88.52 % 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: 1.95 (0.20), residues: 1715 helix: 1.88 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 94 HIS 0.005 0.001 HIS A 115 PHE 0.022 0.002 PHE E 248 TYR 0.022 0.002 TYR E 97 ARG 0.005 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: B 172 GLU cc_start: 0.7783 (mm-30) cc_final: 0.6489 (mp0) REVERT: E 13 ARG cc_start: 0.7054 (ptp90) cc_final: 0.6824 (mpt180) REVERT: E 19 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: C 13 ARG cc_start: 0.7253 (ptp90) cc_final: 0.6918 (mtt180) REVERT: C 19 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6883 (pp30) REVERT: C 159 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: C 303 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7347 (t0) REVERT: D 13 ARG cc_start: 0.7334 (ptp90) cc_final: 0.6954 (mtt90) REVERT: D 44 MET cc_start: 0.8787 (mmt) cc_final: 0.8436 (mmm) REVERT: D 333 GLU cc_start: 0.7233 (tt0) cc_final: 0.6928 (pm20) outliers start: 18 outliers final: 8 residues processed: 201 average time/residue: 1.5214 time to fit residues: 334.1748 Evaluate side-chains 196 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15945 Z= 0.195 Angle : 0.521 5.286 21375 Z= 0.291 Chirality : 0.038 0.161 2245 Planarity : 0.004 0.029 2530 Dihedral : 16.228 111.398 3271 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.98 % Allowed : 10.49 % Favored : 88.52 % 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: 1.86 (0.20), residues: 1715 helix: 1.87 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.30 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 94 HIS 0.005 0.001 HIS A 115 PHE 0.020 0.002 PHE C 248 TYR 0.024 0.002 TYR A 97 ARG 0.005 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 187 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: B 172 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7584 (mp0) REVERT: E 19 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6587 (pm20) REVERT: C 13 ARG cc_start: 0.7241 (ptp90) cc_final: 0.6885 (mtt180) REVERT: C 303 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7340 (t0) REVERT: C 325 MET cc_start: 0.8778 (mtp) cc_final: 0.8426 (mtp) REVERT: D 13 ARG cc_start: 0.7369 (ptp90) cc_final: 0.6981 (mtt90) REVERT: D 19 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: D 44 MET cc_start: 0.8783 (mmt) cc_final: 0.8549 (mmm) REVERT: D 333 GLU cc_start: 0.7235 (tt0) cc_final: 0.6948 (pm20) outliers start: 15 outliers final: 8 residues processed: 192 average time/residue: 1.6581 time to fit residues: 347.5672 Evaluate side-chains 189 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.2980 chunk 116 optimal weight: 0.0670 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15945 Z= 0.134 Angle : 0.449 5.180 21375 Z= 0.254 Chirality : 0.035 0.159 2245 Planarity : 0.003 0.031 2530 Dihedral : 14.863 105.143 3271 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.11 % Allowed : 10.30 % Favored : 88.59 % 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: 2.09 (0.20), residues: 1715 helix: 2.00 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : -0.25 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 94 HIS 0.004 0.001 HIS A 115 PHE 0.014 0.002 PHE C 171 TYR 0.020 0.001 TYR B 236 ARG 0.004 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 71 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: C 13 ARG cc_start: 0.7179 (ptp90) cc_final: 0.6809 (mtt180) REVERT: C 165 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7086 (mtm-85) REVERT: C 303 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7186 (t0) REVERT: C 325 MET cc_start: 0.8774 (mtp) cc_final: 0.8453 (mtp) REVERT: D 13 ARG cc_start: 0.7283 (ptp90) cc_final: 0.6919 (mtt90) REVERT: D 165 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7272 (mtt-85) REVERT: D 333 GLU cc_start: 0.7248 (tt0) cc_final: 0.7027 (pm20) outliers start: 17 outliers final: 8 residues processed: 207 average time/residue: 1.4600 time to fit residues: 332.1557 Evaluate side-chains 199 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 11 ASN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15945 Z= 0.159 Angle : 0.474 6.129 21375 Z= 0.267 Chirality : 0.036 0.159 2245 Planarity : 0.003 0.031 2530 Dihedral : 14.335 100.757 3271 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.05 % Allowed : 10.36 % Favored : 88.59 % 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: 2.03 (0.20), residues: 1715 helix: 2.01 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.25 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 94 HIS 0.004 0.001 HIS A 115 PHE 0.016 0.002 PHE A 248 TYR 0.022 0.002 TYR C 97 ARG 0.003 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 19 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: E 71 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: C 13 ARG cc_start: 0.7218 (ptp90) cc_final: 0.6858 (mtt180) REVERT: C 19 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6752 (pm20) REVERT: C 325 MET cc_start: 0.8780 (mtp) cc_final: 0.8445 (mtp) REVERT: D 13 ARG cc_start: 0.7329 (ptp90) cc_final: 0.6896 (mtt90) REVERT: D 165 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7312 (mtt-85) REVERT: D 293 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7861 (tm130) REVERT: D 333 GLU cc_start: 0.7267 (tt0) cc_final: 0.7043 (pm20) outliers start: 16 outliers final: 6 residues processed: 196 average time/residue: 1.4689 time to fit residues: 315.8994 Evaluate side-chains 195 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15945 Z= 0.171 Angle : 0.488 6.631 21375 Z= 0.274 Chirality : 0.037 0.160 2245 Planarity : 0.004 0.032 2530 Dihedral : 14.159 97.637 3271 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.18 % Allowed : 10.49 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 1715 helix: 1.96 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.18 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 94 HIS 0.004 0.001 HIS A 115 PHE 0.017 0.002 PHE C 248 TYR 0.023 0.002 TYR C 97 ARG 0.003 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 ARG cc_start: 0.7117 (ptp90) cc_final: 0.6772 (mtt180) REVERT: E 19 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: E 71 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: C 13 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6849 (mtt180) REVERT: C 19 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: C 165 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7099 (mtm-85) REVERT: C 325 MET cc_start: 0.8768 (mtp) cc_final: 0.8393 (mtp) REVERT: D 13 ARG cc_start: 0.7331 (ptp90) cc_final: 0.6909 (mtt90) REVERT: D 19 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: D 165 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7340 (mtt-85) REVERT: D 293 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7869 (tm130) outliers start: 18 outliers final: 7 residues processed: 192 average time/residue: 1.5044 time to fit residues: 317.0443 Evaluate side-chains 199 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15945 Z= 0.138 Angle : 0.453 6.215 21375 Z= 0.256 Chirality : 0.035 0.158 2245 Planarity : 0.003 0.032 2530 Dihedral : 13.665 95.407 3271 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.05 % Allowed : 10.82 % Favored : 88.13 % 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: 2.13 (0.20), residues: 1715 helix: 1.99 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.11 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.003 0.001 HIS E 115 PHE 0.014 0.002 PHE C 171 TYR 0.022 0.001 TYR B 236 ARG 0.003 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: E 71 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: C 13 ARG cc_start: 0.7213 (ptp90) cc_final: 0.6847 (mtt180) REVERT: C 19 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: C 325 MET cc_start: 0.8764 (mtp) cc_final: 0.8417 (mtp) REVERT: D 13 ARG cc_start: 0.7316 (ptp90) cc_final: 0.6895 (mtt90) REVERT: D 165 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7294 (mtt-85) outliers start: 16 outliers final: 8 residues processed: 199 average time/residue: 1.4622 time to fit residues: 319.8565 Evaluate side-chains 199 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15945 Z= 0.162 Angle : 0.479 7.235 21375 Z= 0.269 Chirality : 0.037 0.159 2245 Planarity : 0.003 0.033 2530 Dihedral : 13.492 93.972 3271 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.98 % Allowed : 11.15 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1715 helix: 2.03 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.26 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 94 HIS 0.004 0.001 HIS A 115 PHE 0.016 0.002 PHE A 248 TYR 0.025 0.002 TYR B 236 ARG 0.003 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: E 71 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: C 13 ARG cc_start: 0.7226 (ptp90) cc_final: 0.6854 (mtt180) REVERT: C 19 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: D 13 ARG cc_start: 0.7339 (ptp90) cc_final: 0.6910 (mtt90) REVERT: D 19 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: D 165 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7307 (mtt-85) REVERT: D 293 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7848 (tm130) outliers start: 15 outliers final: 7 residues processed: 194 average time/residue: 1.4828 time to fit residues: 315.7395 Evaluate side-chains 201 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 0.0370 chunk 161 optimal weight: 7.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15945 Z= 0.138 Angle : 0.452 6.986 21375 Z= 0.255 Chirality : 0.035 0.158 2245 Planarity : 0.003 0.032 2530 Dihedral : 12.970 90.946 3271 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.92 % Allowed : 11.28 % Favored : 87.80 % 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: 2.16 (0.20), residues: 1715 helix: 2.05 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : -0.22 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.003 0.001 HIS E 115 PHE 0.018 0.002 PHE E 42 TYR 0.024 0.001 TYR B 236 ARG 0.003 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7101 (ptp90) cc_final: 0.6722 (mtt90) REVERT: B 71 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: E 71 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: C 13 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6843 (mtt180) REVERT: C 19 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: C 303 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7173 (t0) REVERT: C 325 MET cc_start: 0.8747 (mtp) cc_final: 0.8438 (mtp) REVERT: D 13 ARG cc_start: 0.7342 (ptp90) cc_final: 0.6964 (mtm-85) REVERT: D 19 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6474 (pm20) outliers start: 14 outliers final: 6 residues processed: 198 average time/residue: 1.4494 time to fit residues: 315.9124 Evaluate side-chains 201 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15945 Z= 0.159 Angle : 0.477 7.601 21375 Z= 0.268 Chirality : 0.036 0.159 2245 Planarity : 0.003 0.033 2530 Dihedral : 12.847 89.614 3271 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.79 % Allowed : 11.54 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1715 helix: 2.03 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.26 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 287 HIS 0.003 0.001 HIS A 115 PHE 0.020 0.002 PHE E 42 TYR 0.026 0.002 TYR B 236 ARG 0.006 0.000 ARG D 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7108 (ptp90) cc_final: 0.6819 (mtt90) REVERT: B 71 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: E 13 ARG cc_start: 0.7092 (ptp90) cc_final: 0.6723 (mtt90) REVERT: E 71 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: C 13 ARG cc_start: 0.7230 (ptp90) cc_final: 0.6857 (mtt180) REVERT: C 19 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6748 (pm20) REVERT: C 303 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7263 (t0) REVERT: D 13 ARG cc_start: 0.7344 (ptp90) cc_final: 0.6901 (mtt90) REVERT: D 293 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7846 (tm130) outliers start: 12 outliers final: 7 residues processed: 194 average time/residue: 1.4887 time to fit residues: 318.2957 Evaluate side-chains 199 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0020 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107322 restraints weight = 32075.755| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.48 r_work: 0.3191 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15945 Z= 0.212 Angle : 0.536 7.879 21375 Z= 0.297 Chirality : 0.039 0.163 2245 Planarity : 0.004 0.034 2530 Dihedral : 13.206 90.353 3271 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.66 % Allowed : 11.67 % Favored : 87.67 % 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: 1.94 (0.19), residues: 1715 helix: 1.90 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.19 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 287 HIS 0.005 0.001 HIS A 115 PHE 0.024 0.002 PHE E 42 TYR 0.028 0.002 TYR B 236 ARG 0.003 0.000 ARG C 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6090.02 seconds wall clock time: 108 minutes 20.80 seconds (6500.80 seconds total)