Starting phenix.real_space_refine on Fri Aug 2 20:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/08_2024/8ur5_42482.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/08_2024/8ur5_42482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/08_2024/8ur5_42482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/08_2024/8ur5_42482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/08_2024/8ur5_42482.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/08_2024/8ur5_42482.cif" } resolution = 3.7 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= 0.013 sd= 0.124 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 18 5.16 5 C 3282 2.51 5 N 858 2.21 5 O 831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4989 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1607 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 14, 'TRANS': 217} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 11, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "B" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1607 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 14, 'TRANS': 217} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 11, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1607 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 14, 'TRANS': 217} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 11, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.27, per 1000 atoms: 0.66 Number of scatterers: 4989 At special positions: 0 Unit cell: (87.1141, 82.8298, 74.2612, 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 18 16.00 O 831 8.00 N 858 7.00 C 3282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.01 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.01 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 139 " distance=2.02 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 271 " distance=2.05 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.01 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 271 " distance=2.05 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 163 " " NAG A 502 " - " ASN A 129 " " NAG A 503 " - " ASN A 58 " " NAG A 504 " - " ASN A 91 " " NAG B 501 " - " ASN B 163 " " NAG B 502 " - " ASN B 129 " " NAG B 503 " - " ASN B 58 " " NAG B 504 " - " ASN B 91 " " NAG C 501 " - " ASN C 163 " " NAG C 502 " - " ASN C 129 " " NAG C 503 " - " ASN C 58 " " NAG C 504 " - " ASN C 91 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 877.0 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1284 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 16.8% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.996A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.996A pdb=" N TRP B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.997A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 275 through 283 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.625A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.625A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.625A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 175 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.625A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 175 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.624A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.624A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'C' and resid 164 through 169 189 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 753 1.31 - 1.44: 1533 1.44 - 1.57: 2841 1.57 - 1.69: 9 1.69 - 1.82: 18 Bond restraints: 5154 Sorted by residual: bond pdb=" C ARG C 229 " pdb=" O ARG C 229 " ideal model delta sigma weight residual 1.234 1.185 0.048 1.24e-02 6.50e+03 1.53e+01 bond pdb=" C ARG B 229 " pdb=" O ARG B 229 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.24e-02 6.50e+03 1.47e+01 bond pdb=" C ARG A 229 " pdb=" O ARG A 229 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.24e-02 6.50e+03 1.45e+01 bond pdb=" CA ARG B 229 " pdb=" CB ARG B 229 " ideal model delta sigma weight residual 1.533 1.474 0.059 1.66e-02 3.63e+03 1.26e+01 bond pdb=" CA ARG A 229 " pdb=" CB ARG A 229 " ideal model delta sigma weight residual 1.533 1.474 0.059 1.66e-02 3.63e+03 1.26e+01 ... (remaining 5149 not shown) Histogram of bond angle deviations from ideal: 101.64 - 108.07: 350 108.07 - 114.50: 2791 114.50 - 120.93: 2309 120.93 - 127.36: 1594 127.36 - 133.78: 75 Bond angle restraints: 7119 Sorted by residual: angle pdb=" C HIS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta sigma weight residual 119.66 126.85 -7.19 7.30e-01 1.88e+00 9.71e+01 angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.82 -7.16 7.30e-01 1.88e+00 9.63e+01 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.66 126.80 -7.14 7.30e-01 1.88e+00 9.56e+01 angle pdb=" C ASN A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta sigma weight residual 119.85 126.77 -6.92 1.01e+00 9.80e-01 4.70e+01 angle pdb=" C ASN B 88 " pdb=" N PRO B 89 " pdb=" CA PRO B 89 " ideal model delta sigma weight residual 119.85 126.76 -6.91 1.01e+00 9.80e-01 4.68e+01 ... (remaining 7114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.28: 2852 12.28 - 24.55: 115 24.55 - 36.83: 57 36.83 - 49.10: 18 49.10 - 61.38: 9 Dihedral angle restraints: 3051 sinusoidal: 1038 harmonic: 2013 Sorted by residual: dihedral pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " pdb=" SG CYS B 139 " pdb=" CB CYS B 139 " ideal model delta sinusoidal sigma weight residual 93.00 130.41 -37.41 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual 93.00 130.40 -37.40 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 130.38 -37.38 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 3048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 529 0.067 - 0.133: 230 0.133 - 0.200: 27 0.200 - 0.267: 33 0.267 - 0.334: 15 Chirality restraints: 834 Sorted by residual: chirality pdb=" C2 NAG B 501 " pdb=" C1 NAG B 501 " pdb=" C3 NAG B 501 " pdb=" N2 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C2 NAG C 501 " pdb=" C1 NAG C 501 " pdb=" C3 NAG C 501 " pdb=" N2 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C2 NAG A 501 " pdb=" C1 NAG A 501 " pdb=" C3 NAG A 501 " pdb=" N2 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 831 not shown) Planarity restraints: 912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 92 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C GLY C 92 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY C 92 " -0.019 2.00e-02 2.50e+03 pdb=" N THR C 93 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 92 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C GLY A 92 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A 92 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A 93 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 92 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C GLY B 92 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY B 92 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 93 " 0.017 2.00e-02 2.50e+03 ... (remaining 909 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2582 2.99 - 3.47: 4265 3.47 - 3.94: 7952 3.94 - 4.42: 8647 4.42 - 4.90: 14219 Nonbonded interactions: 37665 Sorted by model distance: nonbonded pdb=" OD1 ASN B 163 " pdb=" N2 NAG B 501 " model vdw 2.510 3.120 nonbonded pdb=" OD1 ASN A 163 " pdb=" N2 NAG A 501 " model vdw 2.510 3.120 nonbonded pdb=" OD1 ASN C 163 " pdb=" N2 NAG C 501 " model vdw 2.510 3.120 nonbonded pdb=" O ILE A 275 " pdb=" N GLU A 278 " model vdw 2.541 3.120 nonbonded pdb=" O ILE B 275 " pdb=" N GLU B 278 " model vdw 2.541 3.120 ... (remaining 37660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.810 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.011 0.060 5154 Z= 0.725 Angle : 1.447 7.787 7119 Z= 1.011 Chirality : 0.089 0.334 834 Planarity : 0.005 0.029 900 Dihedral : 9.297 51.962 1740 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.35 % Favored : 95.22 % Rotamer: Outliers : 1.71 % Allowed : 3.42 % Favored : 94.87 % 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: -0.71 (0.29), residues: 690 helix: -2.02 (0.42), residues: 117 sheet: 2.31 (0.34), residues: 171 loop : -1.32 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 80 HIS 0.004 0.001 HIS C 130 PHE 0.010 0.002 PHE C 115 TYR 0.027 0.004 TYR B 195 ARG 0.002 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 0.510 Fit side-chains REVERT: A 229 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7726 (mtm110) REVERT: A 230 ILE cc_start: 0.9278 (tt) cc_final: 0.9013 (tt) REVERT: A 256 TYR cc_start: 0.8142 (m-80) cc_final: 0.7753 (m-10) REVERT: B 229 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7723 (mtm110) REVERT: B 256 TYR cc_start: 0.7999 (m-80) cc_final: 0.7524 (m-10) REVERT: C 155 THR cc_start: 0.6919 (p) cc_final: 0.6688 (t) REVERT: C 229 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7594 (mtm110) REVERT: C 256 TYR cc_start: 0.7957 (m-80) cc_final: 0.7540 (m-10) outliers start: 6 outliers final: 1 residues processed: 170 average time/residue: 0.2130 time to fit residues: 43.7241 Evaluate side-chains 106 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain C residue 229 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.0010 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5154 Z= 0.252 Angle : 0.704 8.050 7119 Z= 0.361 Chirality : 0.054 0.628 834 Planarity : 0.005 0.022 900 Dihedral : 7.040 57.451 1012 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.33 % Favored : 96.23 % Rotamer: Outliers : 3.99 % Allowed : 18.80 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.31), residues: 690 helix: -1.35 (0.48), residues: 117 sheet: 1.92 (0.35), residues: 180 loop : -0.47 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 153 HIS 0.004 0.001 HIS C 184 PHE 0.025 0.002 PHE C 147 TYR 0.016 0.002 TYR B 82 ARG 0.002 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.535 Fit side-chains REVERT: A 95 PHE cc_start: 0.8431 (t80) cc_final: 0.8076 (t80) REVERT: A 224 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7412 (ttm170) REVERT: A 229 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7845 (mtm110) REVERT: A 237 LEU cc_start: 0.8793 (mt) cc_final: 0.8565 (mt) REVERT: A 243 ILE cc_start: 0.8725 (tp) cc_final: 0.8466 (tt) REVERT: A 256 TYR cc_start: 0.8299 (m-80) cc_final: 0.7823 (m-10) REVERT: B 191 GLN cc_start: 0.7823 (tp40) cc_final: 0.7295 (tp40) REVERT: B 229 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7857 (mtm110) REVERT: B 256 TYR cc_start: 0.8161 (m-80) cc_final: 0.7639 (m-10) REVERT: C 155 THR cc_start: 0.6693 (p) cc_final: 0.6439 (t) REVERT: C 229 ARG cc_start: 0.8555 (ttm170) cc_final: 0.7906 (mtm110) REVERT: C 256 TYR cc_start: 0.8064 (m-80) cc_final: 0.7579 (m-10) outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 0.1918 time to fit residues: 30.7223 Evaluate side-chains 109 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.0570 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5154 Z= 0.230 Angle : 0.655 6.764 7119 Z= 0.332 Chirality : 0.053 0.526 834 Planarity : 0.004 0.025 900 Dihedral : 5.980 51.982 1003 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.62 % Favored : 95.94 % Rotamer: Outliers : 4.84 % Allowed : 19.66 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.31), residues: 690 helix: -1.06 (0.49), residues: 117 sheet: 1.45 (0.35), residues: 198 loop : -0.36 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 64 HIS 0.004 0.001 HIS C 196 PHE 0.022 0.002 PHE C 118 TYR 0.018 0.002 TYR C 82 ARG 0.005 0.001 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 191 GLN cc_start: 0.7994 (tp40) cc_final: 0.7486 (tp40) REVERT: A 237 LEU cc_start: 0.8872 (mt) cc_final: 0.8650 (mt) REVERT: A 256 TYR cc_start: 0.8308 (m-80) cc_final: 0.7757 (m-10) REVERT: B 191 GLN cc_start: 0.8067 (tp40) cc_final: 0.7389 (tp40) REVERT: B 229 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7469 (mtm110) REVERT: B 256 TYR cc_start: 0.8270 (m-80) cc_final: 0.7186 (m-10) REVERT: C 80 TRP cc_start: 0.8683 (p90) cc_final: 0.8110 (p90) REVERT: C 229 ARG cc_start: 0.8543 (ttm170) cc_final: 0.7797 (mtm110) REVERT: C 256 TYR cc_start: 0.8111 (m-80) cc_final: 0.7600 (m-10) outliers start: 17 outliers final: 9 residues processed: 121 average time/residue: 0.2166 time to fit residues: 32.4972 Evaluate side-chains 118 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 236 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 55 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 5154 Z= 0.497 Angle : 0.738 7.668 7119 Z= 0.379 Chirality : 0.055 0.487 834 Planarity : 0.005 0.049 900 Dihedral : 6.532 51.667 1003 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.51 % Favored : 94.06 % Rotamer: Outliers : 7.98 % Allowed : 19.94 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.30), residues: 690 helix: -2.26 (0.41), residues: 114 sheet: 0.43 (0.35), residues: 195 loop : -0.41 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 153 HIS 0.005 0.002 HIS C 196 PHE 0.030 0.003 PHE C 118 TYR 0.021 0.003 TYR A 102 ARG 0.006 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LEU cc_start: 0.9022 (mt) cc_final: 0.8719 (mt) REVERT: B 168 TYR cc_start: 0.8212 (t80) cc_final: 0.7888 (t80) REVERT: B 191 GLN cc_start: 0.8429 (tp40) cc_final: 0.7575 (tp40) REVERT: B 229 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7105 (mtm110) REVERT: C 80 TRP cc_start: 0.8767 (p90) cc_final: 0.8246 (p90) REVERT: C 229 ARG cc_start: 0.8564 (ttm170) cc_final: 0.7714 (mtm110) outliers start: 28 outliers final: 17 residues processed: 106 average time/residue: 0.2189 time to fit residues: 28.6213 Evaluate side-chains 104 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 244 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5154 Z= 0.319 Angle : 0.663 11.007 7119 Z= 0.331 Chirality : 0.053 0.538 834 Planarity : 0.004 0.031 900 Dihedral : 6.331 49.321 1003 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.93 % Favored : 94.49 % Rotamer: Outliers : 6.55 % Allowed : 23.93 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.30), residues: 690 helix: -1.67 (0.46), residues: 114 sheet: 0.32 (0.34), residues: 195 loop : -0.54 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 153 HIS 0.005 0.001 HIS C 196 PHE 0.022 0.002 PHE C 118 TYR 0.025 0.002 TYR C 168 ARG 0.006 0.001 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: B 168 TYR cc_start: 0.8228 (t80) cc_final: 0.7876 (t80) REVERT: B 191 GLN cc_start: 0.8519 (tp40) cc_final: 0.7650 (tp40) REVERT: B 229 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6994 (mtm110) REVERT: B 232 TYR cc_start: 0.8664 (m-80) cc_final: 0.8271 (m-10) REVERT: B 237 LEU cc_start: 0.8968 (mt) cc_final: 0.8707 (mt) REVERT: C 80 TRP cc_start: 0.8659 (p90) cc_final: 0.8332 (p90) REVERT: C 172 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8620 (mttp) REVERT: C 229 ARG cc_start: 0.8553 (ttm170) cc_final: 0.7785 (mtm110) REVERT: C 274 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7654 (t-90) outliers start: 23 outliers final: 14 residues processed: 108 average time/residue: 0.1890 time to fit residues: 25.3450 Evaluate side-chains 105 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5154 Z= 0.188 Angle : 0.645 10.540 7119 Z= 0.316 Chirality : 0.050 0.481 834 Planarity : 0.004 0.029 900 Dihedral : 6.243 47.436 1003 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.35 % Favored : 95.07 % Rotamer: Outliers : 4.84 % Allowed : 25.36 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.31), residues: 690 helix: -1.15 (0.50), residues: 114 sheet: 0.66 (0.36), residues: 180 loop : -0.60 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.006 0.001 HIS C 196 PHE 0.019 0.002 PHE A 118 TYR 0.026 0.001 TYR C 168 ARG 0.005 0.001 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 58 ASN cc_start: 0.5689 (t0) cc_final: 0.5482 (t0) REVERT: A 64 TRP cc_start: 0.8967 (OUTLIER) cc_final: 0.8587 (t-100) REVERT: A 237 LEU cc_start: 0.9009 (mt) cc_final: 0.8653 (mt) REVERT: B 168 TYR cc_start: 0.8281 (t80) cc_final: 0.7823 (t80) REVERT: B 191 GLN cc_start: 0.8427 (tp40) cc_final: 0.7451 (tp40) REVERT: B 229 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.6823 (mtm110) REVERT: C 80 TRP cc_start: 0.8593 (p90) cc_final: 0.8360 (p90) REVERT: C 229 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7686 (mtm110) REVERT: C 256 TYR cc_start: 0.8141 (m-80) cc_final: 0.7896 (m-10) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.2009 time to fit residues: 26.6844 Evaluate side-chains 103 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.0970 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5154 Z= 0.192 Angle : 0.640 10.004 7119 Z= 0.315 Chirality : 0.048 0.407 834 Planarity : 0.004 0.030 900 Dihedral : 5.908 46.078 1003 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.06 % Favored : 95.36 % Rotamer: Outliers : 5.98 % Allowed : 25.07 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.31), residues: 690 helix: -1.10 (0.51), residues: 111 sheet: 0.78 (0.37), residues: 180 loop : -0.61 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 127 HIS 0.005 0.001 HIS C 196 PHE 0.019 0.002 PHE A 118 TYR 0.029 0.001 TYR C 168 ARG 0.012 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8971 (OUTLIER) cc_final: 0.8602 (t-100) REVERT: A 237 LEU cc_start: 0.9012 (mt) cc_final: 0.8639 (mt) REVERT: B 168 TYR cc_start: 0.8259 (t80) cc_final: 0.7782 (t80) REVERT: B 191 GLN cc_start: 0.8476 (tp40) cc_final: 0.7457 (tp40) REVERT: B 229 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.6603 (mtm110) REVERT: B 232 TYR cc_start: 0.8628 (m-80) cc_final: 0.8318 (m-10) REVERT: C 80 TRP cc_start: 0.8609 (p90) cc_final: 0.8357 (p90) REVERT: C 229 ARG cc_start: 0.8423 (ttm170) cc_final: 0.7406 (mtm-85) REVERT: C 256 TYR cc_start: 0.8203 (m-80) cc_final: 0.7841 (m-10) REVERT: C 274 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.6543 (t70) outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.1803 time to fit residues: 24.7938 Evaluate side-chains 106 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5154 Z= 0.407 Angle : 0.694 10.603 7119 Z= 0.351 Chirality : 0.052 0.483 834 Planarity : 0.004 0.042 900 Dihedral : 6.198 48.161 1003 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.87 % Allowed : 4.35 % Favored : 94.78 % Rotamer: Outliers : 5.13 % Allowed : 25.64 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.30), residues: 690 helix: -1.26 (0.50), residues: 105 sheet: 0.63 (0.37), residues: 180 loop : -0.94 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 153 HIS 0.006 0.001 HIS C 196 PHE 0.020 0.002 PHE A 118 TYR 0.036 0.002 TYR C 232 ARG 0.009 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8977 (OUTLIER) cc_final: 0.8615 (t-100) REVERT: A 237 LEU cc_start: 0.9067 (mt) cc_final: 0.8704 (mt) REVERT: B 168 TYR cc_start: 0.8345 (t80) cc_final: 0.7608 (t80) REVERT: B 191 GLN cc_start: 0.8451 (tp40) cc_final: 0.7405 (tp40) REVERT: B 229 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7033 (mtm110) REVERT: B 232 TYR cc_start: 0.8753 (m-80) cc_final: 0.8542 (m-10) REVERT: C 80 TRP cc_start: 0.8665 (p90) cc_final: 0.8311 (p90) REVERT: C 229 ARG cc_start: 0.8541 (ttm170) cc_final: 0.7446 (mtm-85) REVERT: C 274 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.6857 (t70) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 0.2073 time to fit residues: 25.7926 Evaluate side-chains 100 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5154 Z= 0.304 Angle : 0.662 10.107 7119 Z= 0.331 Chirality : 0.048 0.302 834 Planarity : 0.004 0.042 900 Dihedral : 6.174 47.734 1003 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.91 % Favored : 95.22 % Rotamer: Outliers : 3.99 % Allowed : 26.50 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.30), residues: 690 helix: -1.17 (0.51), residues: 105 sheet: 0.57 (0.37), residues: 180 loop : -1.07 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 180 HIS 0.006 0.001 HIS C 196 PHE 0.021 0.002 PHE A 118 TYR 0.034 0.002 TYR C 168 ARG 0.011 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8938 (OUTLIER) cc_final: 0.8538 (t-100) REVERT: A 237 LEU cc_start: 0.9092 (mt) cc_final: 0.8733 (mt) REVERT: B 168 TYR cc_start: 0.8391 (t80) cc_final: 0.7779 (t80) REVERT: B 191 GLN cc_start: 0.8446 (tp40) cc_final: 0.7350 (tp40) REVERT: B 229 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7022 (mtm110) REVERT: C 59 CYS cc_start: 0.4634 (p) cc_final: 0.4273 (p) REVERT: C 80 TRP cc_start: 0.8640 (p90) cc_final: 0.8359 (p90) REVERT: C 229 ARG cc_start: 0.8517 (ttm170) cc_final: 0.7357 (mtm-85) REVERT: C 274 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.6797 (t70) outliers start: 14 outliers final: 7 residues processed: 99 average time/residue: 0.1938 time to fit residues: 23.9436 Evaluate side-chains 99 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5154 Z= 0.189 Angle : 0.626 9.136 7119 Z= 0.308 Chirality : 0.046 0.213 834 Planarity : 0.004 0.049 900 Dihedral : 5.729 45.257 1003 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.48 % Favored : 95.65 % Rotamer: Outliers : 2.28 % Allowed : 27.07 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.31), residues: 690 helix: -1.01 (0.52), residues: 105 sheet: 0.70 (0.38), residues: 180 loop : -1.02 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.006 0.001 HIS C 196 PHE 0.021 0.002 PHE A 118 TYR 0.030 0.002 TYR C 168 ARG 0.012 0.001 ARG B 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8944 (OUTLIER) cc_final: 0.8490 (t-100) REVERT: A 237 LEU cc_start: 0.9102 (mt) cc_final: 0.8739 (mt) REVERT: B 168 TYR cc_start: 0.8362 (t80) cc_final: 0.7747 (t80) REVERT: B 191 GLN cc_start: 0.8462 (tp40) cc_final: 0.7456 (tp40) REVERT: B 229 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6476 (mtm110) REVERT: C 59 CYS cc_start: 0.4538 (p) cc_final: 0.4332 (p) REVERT: C 80 TRP cc_start: 0.8599 (p90) cc_final: 0.8393 (p90) REVERT: C 152 LEU cc_start: 0.7823 (mt) cc_final: 0.7565 (mt) REVERT: C 229 ARG cc_start: 0.8455 (ttm170) cc_final: 0.7319 (mtm-85) REVERT: C 256 TYR cc_start: 0.8068 (m-80) cc_final: 0.7726 (m-10) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.2029 time to fit residues: 24.1076 Evaluate side-chains 96 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain C residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 0.0980 chunk 48 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123946 restraints weight = 8182.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123930 restraints weight = 9342.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124982 restraints weight = 6799.567| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5154 Z= 0.217 Angle : 0.632 8.539 7119 Z= 0.313 Chirality : 0.046 0.209 834 Planarity : 0.004 0.046 900 Dihedral : 5.537 42.818 1003 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.62 % Favored : 95.51 % Rotamer: Outliers : 2.56 % Allowed : 27.64 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 690 helix: -0.93 (0.53), residues: 105 sheet: 0.79 (0.38), residues: 180 loop : -1.05 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 127 HIS 0.006 0.001 HIS C 196 PHE 0.022 0.002 PHE A 118 TYR 0.028 0.002 TYR C 168 ARG 0.011 0.001 ARG B 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1400.30 seconds wall clock time: 25 minutes 38.19 seconds (1538.19 seconds total)