Starting phenix.real_space_refine on Mon May 6 20:55:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/05_2024/8ur5_42482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/05_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_42482/05_2024/8ur5_42482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/05_2024/8ur5_42482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/05_2024/8ur5_42482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur5_42482/05_2024/8ur5_42482.pdb" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 3.54, per 1000 atoms: 0.71 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.71 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: 1.40 Time building geometry restraints manager: 2.20 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 2.520 nonbonded pdb=" OD1 ASN A 163 " pdb=" N2 NAG A 501 " model vdw 2.510 2.520 nonbonded pdb=" OD1 ASN C 163 " pdb=" N2 NAG C 501 " model vdw 2.510 2.520 nonbonded pdb=" O ILE A 275 " pdb=" N GLU A 278 " model vdw 2.541 2.520 nonbonded pdb=" O ILE B 275 " pdb=" N GLU B 278 " model vdw 2.541 2.520 ... (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 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.530 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.330 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- 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 : 0.650 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: 0.2159 time to fit residues: 44.2818 Evaluate side-chains 106 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.0010 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- 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: 0.7203 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5154 Z= 0.245 Angle : 0.689 6.485 7119 Z= 0.355 Chirality : 0.054 0.646 834 Planarity : 0.004 0.023 900 Dihedral : 7.396 57.409 1012 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.48 % Favored : 96.09 % Rotamer: Outliers : 4.27 % Allowed : 18.52 % 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: 0.04 (0.31), residues: 690 helix: -1.30 (0.48), residues: 117 sheet: 1.94 (0.35), residues: 180 loop : -0.46 (0.29), 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 0.024 0.002 PHE C 147 TYR 0.016 0.002 TYR B 82 ARG 0.002 0.000 ARG A 106 *********************** 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 132 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.545 Fit side-chains REVERT: A 229 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7866 (mtm110) REVERT: A 237 LEU cc_start: 0.8779 (mt) cc_final: 0.8548 (mt) REVERT: A 243 ILE cc_start: 0.8727 (tp) cc_final: 0.8474 (tt) REVERT: A 256 TYR cc_start: 0.8303 (m-80) cc_final: 0.7835 (m-10) REVERT: B 191 GLN cc_start: 0.7789 (tp40) cc_final: 0.7258 (tp40) REVERT: B 229 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7826 (mtm110) REVERT: B 256 TYR cc_start: 0.8152 (m-80) cc_final: 0.7649 (m-10) REVERT: C 155 THR cc_start: 0.6688 (p) cc_final: 0.6438 (t) REVERT: C 229 ARG cc_start: 0.8443 (ttm170) cc_final: 0.7766 (mtm110) REVERT: C 256 TYR cc_start: 0.8060 (m-80) cc_final: 0.7582 (m-10) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.1978 time to fit residues: 31.3020 Evaluate side-chains 108 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5154 Z= 0.205 Angle : 0.621 5.925 7119 Z= 0.318 Chirality : 0.051 0.602 834 Planarity : 0.004 0.024 900 Dihedral : 6.414 51.915 1003 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.75 % Favored : 96.81 % Rotamer: Outliers : 3.70 % Allowed : 21.08 % Favored : 75.21 % 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: 0.14 (0.31), residues: 690 helix: -0.88 (0.50), residues: 114 sheet: 1.56 (0.35), residues: 198 loop : -0.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 80 HIS 0.005 0.001 HIS C 196 PHE 0.021 0.002 PHE C 118 TYR 0.020 0.002 TYR C 232 ARG 0.004 0.000 ARG C 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 119 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.599 Fit side-chains REVERT: A 191 GLN cc_start: 0.7963 (tp40) cc_final: 0.7475 (tp40) REVERT: A 237 LEU cc_start: 0.8861 (mt) cc_final: 0.8635 (mt) REVERT: A 256 TYR cc_start: 0.8299 (m-80) cc_final: 0.7749 (m-10) REVERT: B 191 GLN cc_start: 0.8048 (tp40) cc_final: 0.7314 (tp40) REVERT: B 229 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7355 (mtm110) REVERT: B 256 TYR cc_start: 0.8266 (m-80) cc_final: 0.7169 (m-10) REVERT: C 80 TRP cc_start: 0.8649 (p90) cc_final: 0.8134 (p90) REVERT: C 155 THR cc_start: 0.6779 (p) cc_final: 0.6517 (t) REVERT: C 229 ARG cc_start: 0.8430 (ttm170) cc_final: 0.7682 (mtm110) REVERT: C 256 TYR cc_start: 0.8077 (m-80) cc_final: 0.7579 (m-10) outliers start: 13 outliers final: 9 residues processed: 115 average time/residue: 0.2089 time to fit residues: 29.7184 Evaluate side-chains 115 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 95 PHE 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: 10.0000 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 5154 Z= 0.563 Angle : 0.751 7.867 7119 Z= 0.388 Chirality : 0.055 0.520 834 Planarity : 0.005 0.036 900 Dihedral : 6.808 53.624 1003 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.65 % Favored : 93.91 % Rotamer: Outliers : 7.69 % Allowed : 19.66 % Favored : 72.65 % 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: -0.78 (0.31), residues: 690 helix: -2.37 (0.42), residues: 114 sheet: 0.61 (0.35), residues: 195 loop : -0.45 (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 B 184 PHE 0.031 0.003 PHE C 118 TYR 0.028 0.003 TYR C 232 ARG 0.006 0.001 ARG B 106 *********************** 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 120 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.569 Fit side-chains REVERT: A 237 LEU cc_start: 0.9034 (mt) cc_final: 0.8747 (mt) REVERT: B 168 TYR cc_start: 0.8229 (t80) cc_final: 0.7858 (t80) REVERT: B 191 GLN cc_start: 0.8399 (tp40) cc_final: 0.7586 (tp40) REVERT: B 229 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7246 (mtm110) REVERT: B 232 TYR cc_start: 0.8754 (m-80) cc_final: 0.8505 (m-10) REVERT: C 229 ARG cc_start: 0.8467 (ttm170) cc_final: 0.7681 (mtm110) REVERT: C 256 TYR cc_start: 0.8304 (m-80) cc_final: 0.7926 (m-10) outliers start: 27 outliers final: 16 residues processed: 110 average time/residue: 0.1911 time to fit residues: 26.1891 Evaluate side-chains 109 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 27 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7377 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5154 Z= 0.191 Angle : 0.629 9.447 7119 Z= 0.310 Chirality : 0.051 0.597 834 Planarity : 0.004 0.032 900 Dihedral : 6.569 49.284 1003 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.49 % Favored : 95.07 % 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 : 0.46 % 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: -0.50 (0.31), residues: 690 helix: -1.53 (0.48), residues: 114 sheet: 0.62 (0.35), residues: 195 loop : -0.38 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 153 HIS 0.005 0.001 HIS C 196 PHE 0.021 0.002 PHE C 118 TYR 0.023 0.002 TYR C 168 ARG 0.007 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 123 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 237 LEU cc_start: 0.9008 (mt) cc_final: 0.8693 (mt) REVERT: A 256 TYR cc_start: 0.8283 (m-80) cc_final: 0.7817 (m-10) REVERT: B 118 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6160 (p90) REVERT: B 168 TYR cc_start: 0.8155 (t80) cc_final: 0.7898 (t80) REVERT: B 191 GLN cc_start: 0.8366 (tp40) cc_final: 0.7532 (tp40) REVERT: B 229 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6890 (mtm110) REVERT: B 237 LEU cc_start: 0.9069 (mt) cc_final: 0.8834 (mt) REVERT: B 256 TYR cc_start: 0.8427 (m-80) cc_final: 0.7709 (m-80) REVERT: C 80 TRP cc_start: 0.8683 (p90) cc_final: 0.8220 (p90) REVERT: C 191 GLN cc_start: 0.8455 (tp40) cc_final: 0.7528 (tp40) REVERT: C 229 ARG cc_start: 0.8407 (ttm170) cc_final: 0.7690 (mtm110) REVERT: C 256 TYR cc_start: 0.8203 (m-80) cc_final: 0.7951 (m-10) outliers start: 21 outliers final: 10 residues processed: 116 average time/residue: 0.1915 time to fit residues: 27.7750 Evaluate side-chains 104 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 95 PHE Chi-restraints excluded: chain B residue 118 PHE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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: 0.7401 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5154 Z= 0.244 Angle : 0.629 8.408 7119 Z= 0.312 Chirality : 0.052 0.546 834 Planarity : 0.004 0.028 900 Dihedral : 6.417 48.775 1003 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.64 % Favored : 94.93 % Rotamer: Outliers : 5.41 % Allowed : 26.21 % Favored : 68.38 % 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: -0.47 (0.31), residues: 690 helix: -1.26 (0.50), residues: 114 sheet: 0.60 (0.35), residues: 195 loop : -0.43 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 153 HIS 0.004 0.001 HIS C 196 PHE 0.027 0.002 PHE C 118 TYR 0.022 0.002 TYR C 168 ARG 0.006 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 114 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8951 (OUTLIER) cc_final: 0.8551 (t-100) REVERT: A 237 LEU cc_start: 0.8997 (mt) cc_final: 0.8639 (mt) REVERT: B 118 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.6350 (p90) REVERT: B 168 TYR cc_start: 0.8224 (t80) cc_final: 0.7877 (t80) REVERT: B 191 GLN cc_start: 0.8479 (tp40) cc_final: 0.7606 (tp40) REVERT: B 229 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6850 (mtm110) REVERT: B 232 TYR cc_start: 0.8671 (m-80) cc_final: 0.8385 (m-10) REVERT: B 237 LEU cc_start: 0.9059 (mt) cc_final: 0.8795 (mt) REVERT: C 80 TRP cc_start: 0.8636 (p90) cc_final: 0.8237 (p90) REVERT: C 172 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8575 (mttp) REVERT: C 229 ARG cc_start: 0.8395 (ttm170) cc_final: 0.7693 (mtm110) REVERT: C 256 TYR cc_start: 0.8229 (m-80) cc_final: 0.7877 (m-10) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 0.1977 time to fit residues: 26.1730 Evaluate side-chains 104 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 282 LEU 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 C residue 54 LEU Chi-restraints excluded: chain C residue 65 ILE 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 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.7417 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5154 Z= 0.281 Angle : 0.661 9.080 7119 Z= 0.328 Chirality : 0.052 0.504 834 Planarity : 0.004 0.029 900 Dihedral : 6.304 48.866 1003 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.78 % Favored : 94.78 % Rotamer: Outliers : 5.70 % Allowed : 26.78 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -0.48 (0.31), residues: 690 helix: -1.06 (0.50), residues: 114 sheet: 0.51 (0.36), residues: 195 loop : -0.46 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 153 HIS 0.006 0.001 HIS C 196 PHE 0.024 0.002 PHE C 118 TYR 0.029 0.002 TYR C 168 ARG 0.004 0.001 ARG A 106 *********************** 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 110 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.8603 (t-100) REVERT: A 237 LEU cc_start: 0.9028 (mt) cc_final: 0.8654 (mt) REVERT: B 168 TYR cc_start: 0.8295 (t80) cc_final: 0.7796 (t80) REVERT: B 191 GLN cc_start: 0.8542 (tp40) cc_final: 0.7666 (tp40) REVERT: B 229 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7014 (mtm110) REVERT: B 232 TYR cc_start: 0.8702 (m-80) cc_final: 0.8441 (m-10) REVERT: B 237 LEU cc_start: 0.8908 (mt) cc_final: 0.8649 (mt) REVERT: C 80 TRP cc_start: 0.8625 (p90) cc_final: 0.8251 (p90) REVERT: C 229 ARG cc_start: 0.8393 (ttm170) cc_final: 0.7680 (mtm110) REVERT: C 256 TYR cc_start: 0.8164 (m-80) cc_final: 0.7922 (m-10) REVERT: C 274 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7471 (t-90) outliers start: 20 outliers final: 13 residues processed: 104 average time/residue: 0.2095 time to fit residues: 27.1450 Evaluate side-chains 102 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU 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 A residue 282 LEU 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 54 LEU Chi-restraints excluded: chain C residue 65 ILE 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 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: 0.9980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.0270 chunk 6 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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: 0.7418 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5154 Z= 0.251 Angle : 0.610 8.613 7119 Z= 0.305 Chirality : 0.046 0.208 834 Planarity : 0.004 0.029 900 Dihedral : 5.837 48.562 1003 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.78 % Favored : 94.78 % Rotamer: Outliers : 5.41 % Allowed : 26.50 % Favored : 68.09 % 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: -0.54 (0.31), residues: 690 helix: -0.87 (0.52), residues: 105 sheet: 0.74 (0.37), residues: 180 loop : -0.71 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 127 HIS 0.005 0.001 HIS C 196 PHE 0.023 0.002 PHE C 118 TYR 0.028 0.002 TYR C 168 ARG 0.003 0.001 ARG A 106 *********************** 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 107 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.9003 (OUTLIER) cc_final: 0.8633 (t-100) REVERT: A 237 LEU cc_start: 0.9056 (mt) cc_final: 0.8656 (mt) REVERT: B 168 TYR cc_start: 0.8303 (t80) cc_final: 0.7730 (t80) REVERT: B 191 GLN cc_start: 0.8417 (tp40) cc_final: 0.7446 (tp40) REVERT: B 229 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.6900 (mtm110) REVERT: B 232 TYR cc_start: 0.8679 (m-80) cc_final: 0.8385 (m-10) REVERT: B 237 LEU cc_start: 0.8937 (mt) cc_final: 0.8662 (mt) REVERT: C 80 TRP cc_start: 0.8685 (p90) cc_final: 0.8368 (p90) REVERT: C 82 TYR cc_start: 0.6103 (m-80) cc_final: 0.5727 (m-80) REVERT: C 152 LEU cc_start: 0.7909 (mt) cc_final: 0.7635 (mt) REVERT: C 229 ARG cc_start: 0.8383 (ttm170) cc_final: 0.7413 (mtm-85) REVERT: C 274 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.6631 (t70) outliers start: 19 outliers final: 12 residues processed: 100 average time/residue: 0.2176 time to fit residues: 26.7016 Evaluate side-chains 100 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 54 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 244 ILE 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: 0.0770 chunk 48 optimal weight: 0.0070 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5154 Z= 0.174 Angle : 0.590 8.152 7119 Z= 0.292 Chirality : 0.047 0.338 834 Planarity : 0.004 0.043 900 Dihedral : 5.650 47.254 1003 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.35 % Favored : 95.22 % Rotamer: Outliers : 3.70 % Allowed : 27.92 % Favored : 68.38 % 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: -0.43 (0.31), residues: 690 helix: -0.71 (0.53), residues: 105 sheet: 0.90 (0.38), residues: 180 loop : -0.71 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 127 HIS 0.006 0.001 HIS C 196 PHE 0.022 0.002 PHE A 118 TYR 0.030 0.001 TYR C 168 ARG 0.012 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 99 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.9004 (OUTLIER) cc_final: 0.8625 (t-100) REVERT: A 237 LEU cc_start: 0.9053 (mt) cc_final: 0.8667 (mt) REVERT: B 168 TYR cc_start: 0.8358 (t80) cc_final: 0.7824 (t80) REVERT: B 191 GLN cc_start: 0.8425 (tp40) cc_final: 0.7447 (tp40) REVERT: B 229 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6795 (mtm110) REVERT: B 232 TYR cc_start: 0.8641 (m-80) cc_final: 0.8418 (m-10) REVERT: C 80 TRP cc_start: 0.8635 (p90) cc_final: 0.8312 (p90) REVERT: C 82 TYR cc_start: 0.6140 (m-80) cc_final: 0.5832 (m-80) REVERT: C 152 LEU cc_start: 0.7828 (mt) cc_final: 0.7567 (mt) REVERT: C 229 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7381 (mtm-85) REVERT: C 256 TYR cc_start: 0.8238 (m-80) cc_final: 0.7925 (m-10) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.2004 time to fit residues: 24.0170 Evaluate side-chains 94 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 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 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 54 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 236 LEU 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: 0.4980 chunk 63 optimal weight: 0.6980 chunk 54 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 50 optimal weight: 0.0980 chunk 8 optimal weight: 20.0000 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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: 0.7347 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5154 Z= 0.149 Angle : 0.584 7.661 7119 Z= 0.288 Chirality : 0.044 0.147 834 Planarity : 0.004 0.054 900 Dihedral : 5.221 45.364 1003 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.91 % Favored : 95.65 % Rotamer: Outliers : 1.99 % Allowed : 29.63 % Favored : 68.38 % 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: -0.30 (0.32), residues: 690 helix: -0.47 (0.54), residues: 105 sheet: 1.02 (0.39), residues: 180 loop : -0.68 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 127 HIS 0.006 0.001 HIS C 196 PHE 0.021 0.002 PHE A 118 TYR 0.027 0.001 TYR C 168 ARG 0.013 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 97 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.8652 (t-100) REVERT: A 237 LEU cc_start: 0.9151 (mt) cc_final: 0.8827 (mt) REVERT: B 168 TYR cc_start: 0.8358 (t80) cc_final: 0.7756 (t80) REVERT: B 191 GLN cc_start: 0.8448 (tp40) cc_final: 0.7577 (tp40) REVERT: B 229 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.6829 (mtm110) REVERT: B 232 TYR cc_start: 0.8683 (m-80) cc_final: 0.8480 (m-10) REVERT: C 80 TRP cc_start: 0.8632 (p90) cc_final: 0.8385 (p90) REVERT: C 152 LEU cc_start: 0.7841 (mt) cc_final: 0.7588 (mt) REVERT: C 229 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7321 (mtm-85) REVERT: C 256 TYR cc_start: 0.8121 (m-80) cc_final: 0.7798 (m-10) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2015 time to fit residues: 23.6215 Evaluate side-chains 93 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 155 THR 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 15 optimal weight: 4.9990 chunk 54 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.0060 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 overall best weight: 0.4410 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.161365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128392 restraints weight = 8223.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128332 restraints weight = 8803.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129893 restraints weight = 6606.400| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5154 Z= 0.148 Angle : 0.572 7.191 7119 Z= 0.282 Chirality : 0.044 0.134 834 Planarity : 0.004 0.059 900 Dihedral : 4.929 43.652 1003 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.33 % Favored : 96.23 % Rotamer: Outliers : 1.42 % Allowed : 29.91 % Favored : 68.66 % 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: -0.12 (0.32), residues: 690 helix: -0.31 (0.55), residues: 105 sheet: 1.16 (0.39), residues: 180 loop : -0.58 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 127 HIS 0.006 0.001 HIS C 196 PHE 0.020 0.002 PHE A 118 TYR 0.024 0.001 TYR C 168 ARG 0.012 0.001 ARG A 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1386.57 seconds wall clock time: 26 minutes 3.20 seconds (1563.20 seconds total)