Starting phenix.real_space_refine on Thu Mar 21 16:49:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j00_35879/03_2024/8j00_35879_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j00_35879/03_2024/8j00_35879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j00_35879/03_2024/8j00_35879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j00_35879/03_2024/8j00_35879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j00_35879/03_2024/8j00_35879_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j00_35879/03_2024/8j00_35879_neut_trim_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 9876 2.51 5 N 2560 2.21 5 O 2716 1.98 5 H 14944 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30184 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.76, per 1000 atoms: 0.42 Number of scatterers: 30184 At special positions: 0 Unit cell: (127.41, 127.41, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 O 2716 8.00 N 2560 7.00 C 9876 6.00 H 14944 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.38 Conformation dependent library (CDL) restraints added in 3.2 seconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 91 through 114 Processing helix chain 'A' and resid 119 through 150 removed outlier: 3.972A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N CYS A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 254 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 326 removed outlier: 4.239A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 334 through 349 Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 565 through 594 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 119 through 150 removed outlier: 3.960A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N CYS B 150 " --> pdb=" O TRP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 254 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 328 removed outlier: 4.239A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 4.331A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 349 Processing helix chain 'B' and resid 542 through 560 Processing helix chain 'B' and resid 565 through 594 Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 91 through 114 Processing helix chain 'C' and resid 119 through 150 removed outlier: 3.868A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N CYS C 150 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 254 Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'C' and resid 288 through 328 removed outlier: 4.241A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix removed outlier: 4.343A pdb=" N HIS C 328 " --> pdb=" O HIS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 542 through 560 Processing helix chain 'C' and resid 565 through 594 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 91 through 114 Processing helix chain 'D' and resid 119 through 150 removed outlier: 3.857A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N CYS D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 216 through 254 removed outlier: 5.304A pdb=" N LYS D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 328 removed outlier: 4.239A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 4.369A pdb=" N HIS D 328 " --> pdb=" O HIS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 349 Processing helix chain 'D' and resid 542 through 560 Processing helix chain 'D' and resid 565 through 594 Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 141 through 147 Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 30 through 40 Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 83 through 93 Processing helix chain 'G' and resid 103 through 112 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 141 through 147 Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 73 Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 140 through 147 1037 hydrogen bonds defined for protein. 2859 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: 10.36 Time building geometry restraints manager: 24.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14916 1.03 - 1.23: 76 1.23 - 1.43: 6640 1.43 - 1.62: 8708 1.62 - 1.82: 164 Bond restraints: 30504 Sorted by residual: bond pdb=" C07 P0T C 802 " pdb=" C09 P0T C 802 " ideal model delta sigma weight residual 1.336 1.601 -0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C07 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sigma weight residual 1.336 1.600 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C07 P0T B 802 " pdb=" C09 P0T B 802 " ideal model delta sigma weight residual 1.336 1.599 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C07 P0T A 802 " pdb=" C09 P0T A 802 " ideal model delta sigma weight residual 1.336 1.599 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C07 P0T B 801 " pdb=" C09 P0T B 801 " ideal model delta sigma weight residual 1.336 1.596 -0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 30499 not shown) Histogram of bond angle deviations from ideal: 81.89 - 92.32: 8 92.32 - 102.75: 60 102.75 - 113.18: 34754 113.18 - 123.61: 17537 123.61 - 134.04: 2461 Bond angle restraints: 54820 Sorted by residual: angle pdb=" C07 P0T D 801 " pdb=" C04 P0T D 801 " pdb=" C08 P0T D 801 " ideal model delta sigma weight residual 112.03 81.89 30.14 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C07 P0T C 801 " pdb=" C04 P0T C 801 " pdb=" C08 P0T C 801 " ideal model delta sigma weight residual 112.03 81.91 30.12 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C07 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C08 P0T A 801 " ideal model delta sigma weight residual 112.03 81.93 30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C07 P0T B 801 " pdb=" C04 P0T B 801 " pdb=" C08 P0T B 801 " ideal model delta sigma weight residual 112.03 81.96 30.07 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C07 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C08 P0T B 802 " ideal model delta sigma weight residual 112.03 83.66 28.37 3.00e+00 1.11e-01 8.94e+01 ... (remaining 54815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 12876 23.07 - 46.15: 1091 46.15 - 69.22: 290 69.22 - 92.30: 27 92.30 - 115.37: 24 Dihedral angle restraints: 14308 sinusoidal: 7692 harmonic: 6616 Sorted by residual: dihedral pdb=" CA ARG B 560 " pdb=" C ARG B 560 " pdb=" N PRO B 561 " pdb=" CA PRO B 561 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C03 P0T D 801 " pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " pdb=" C09 P0T D 801 " ideal model delta sinusoidal sigma weight residual 49.00 -66.37 115.37 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C03 P0T C 801 " pdb=" C05 P0T C 801 " pdb=" C06 P0T C 801 " pdb=" C09 P0T C 801 " ideal model delta sinusoidal sigma weight residual 49.00 -66.37 115.37 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 14305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1530 0.026 - 0.053: 526 0.053 - 0.079: 164 0.079 - 0.105: 63 0.105 - 0.131: 13 Chirality restraints: 2296 Sorted by residual: chirality pdb=" CB THR A 298 " pdb=" CA THR A 298 " pdb=" OG1 THR A 298 " pdb=" CG2 THR A 298 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CB THR C 298 " pdb=" CA THR C 298 " pdb=" OG1 THR C 298 " pdb=" CG2 THR C 298 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE G 64 " pdb=" N ILE G 64 " pdb=" C ILE G 64 " pdb=" CB ILE G 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 2293 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 130 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" CD GLU D 130 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU D 130 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 130 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 130 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" CD GLU A 130 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU A 130 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 130 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 97 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ALA D 97 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA D 97 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR D 98 " -0.008 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1663 2.16 - 2.77: 58616 2.77 - 3.38: 89874 3.38 - 3.99: 106612 3.99 - 4.60: 168699 Nonbonded interactions: 425464 Sorted by model distance: nonbonded pdb=" HG1 THR H 118 " pdb=" OE1 GLU H 121 " model vdw 1.552 1.850 nonbonded pdb=" HG1 THR F 118 " pdb=" OE1 GLU F 121 " model vdw 1.555 1.850 nonbonded pdb=" O LEU D 272 " pdb=" HG1 THR D 276 " model vdw 1.556 1.850 nonbonded pdb=" O LEU A 272 " pdb=" HG1 THR A 276 " model vdw 1.557 1.850 nonbonded pdb=" HG1 THR E 118 " pdb=" OE1 GLU E 121 " model vdw 1.560 1.850 ... (remaining 425459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.460 Extract box with map and model: 4.610 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 93.030 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 0.265 15560 Z= 0.744 Angle : 0.917 30.140 20980 Z= 0.390 Chirality : 0.032 0.131 2296 Planarity : 0.003 0.031 2636 Dihedral : 19.379 115.375 5760 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.06 % Allowed : 29.00 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1844 helix: 1.99 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 288 HIS 0.003 0.001 HIS F 108 PHE 0.014 0.001 PHE D 297 TYR 0.012 0.001 TYR C 571 ARG 0.006 0.000 ARG B 553 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8796 (m-40) cc_final: 0.8332 (t0) REVERT: C 130 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7212 (tm-30) REVERT: D 123 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7932 (tm-30) REVERT: D 130 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 106 LEU cc_start: 0.8830 (tp) cc_final: 0.8609 (tp) REVERT: E 145 MET cc_start: 0.6369 (tmm) cc_final: 0.5872 (ptt) REVERT: F 141 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7593 (tm-30) REVERT: G 77 MET cc_start: 0.1188 (tpp) cc_final: 0.0662 (tpp) REVERT: H 73 MET cc_start: -0.2510 (mmt) cc_final: -0.2766 (ttm) outliers start: 1 outliers final: 4 residues processed: 243 average time/residue: 2.0245 time to fit residues: 559.4169 Evaluate side-chains 203 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.7138 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15560 Z= 0.164 Angle : 0.546 8.054 20980 Z= 0.269 Chirality : 0.032 0.146 2296 Planarity : 0.003 0.047 2636 Dihedral : 10.838 80.967 2244 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.71 % Allowed : 29.51 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.20), residues: 1844 helix: 2.13 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.32 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 288 HIS 0.002 0.000 HIS H 108 PHE 0.014 0.001 PHE F 142 TYR 0.006 0.001 TYR D 237 ARG 0.007 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 224 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8834 (m-40) cc_final: 0.8625 (m110) REVERT: C 123 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7905 (tm-30) REVERT: C 130 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7263 (tm-30) REVERT: D 123 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7902 (tm-30) REVERT: D 130 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7373 (tm-30) REVERT: E 73 MET cc_start: -0.2669 (mmt) cc_final: -0.3367 (ttm) REVERT: F 141 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7610 (tm-30) REVERT: G 77 MET cc_start: 0.1203 (tpp) cc_final: 0.0606 (tpp) REVERT: H 73 MET cc_start: -0.2569 (mmt) cc_final: -0.2832 (ttm) outliers start: 27 outliers final: 14 residues processed: 240 average time/residue: 2.0477 time to fit residues: 558.6540 Evaluate side-chains 226 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 134 optimal weight: 50.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15560 Z= 0.282 Angle : 0.535 7.141 20980 Z= 0.278 Chirality : 0.032 0.120 2296 Planarity : 0.003 0.027 2636 Dihedral : 6.935 38.587 2240 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.30 % Allowed : 28.11 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.20), residues: 1844 helix: 2.06 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.34 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 270 HIS 0.001 0.000 HIS D 575 PHE 0.013 0.001 PHE A 80 TYR 0.009 0.001 TYR B 74 ARG 0.004 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 222 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8787 (m-40) cc_final: 0.8570 (m110) REVERT: C 130 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7252 (tm-30) REVERT: D 123 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7992 (tm-30) REVERT: D 130 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7364 (tm-30) REVERT: D 579 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7807 (tp) REVERT: E 51 ASP cc_start: 0.8385 (t0) cc_final: 0.8177 (t0) REVERT: E 73 MET cc_start: -0.2754 (mmt) cc_final: -0.3367 (ttm) REVERT: F 141 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7596 (tm-30) REVERT: F 145 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.6076 (ptt) REVERT: G 77 MET cc_start: 0.0881 (OUTLIER) cc_final: 0.0212 (tpp) REVERT: H 73 MET cc_start: -0.2501 (mmt) cc_final: -0.2799 (ttm) outliers start: 52 outliers final: 23 residues processed: 258 average time/residue: 1.9907 time to fit residues: 584.2787 Evaluate side-chains 231 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS G 144 GLN H 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15560 Z= 0.183 Angle : 0.489 7.170 20980 Z= 0.256 Chirality : 0.031 0.122 2296 Planarity : 0.003 0.027 2636 Dihedral : 5.793 28.048 2240 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.73 % Allowed : 28.36 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.20), residues: 1844 helix: 2.20 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.32 (0.37), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.010 0.001 HIS H 108 PHE 0.015 0.001 PHE F 142 TYR 0.008 0.001 TYR C 127 ARG 0.006 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8780 (m-40) cc_final: 0.8310 (t0) REVERT: C 123 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7944 (tm-30) REVERT: C 130 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7285 (tm-30) REVERT: D 123 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7939 (tm-30) REVERT: D 130 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7421 (tm-30) REVERT: E 51 ASP cc_start: 0.8384 (t0) cc_final: 0.8134 (t0) REVERT: E 73 MET cc_start: -0.2658 (mmt) cc_final: -0.3245 (ttm) REVERT: F 141 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7572 (tm-30) REVERT: F 145 MET cc_start: 0.6386 (ptt) cc_final: 0.6098 (ptt) REVERT: G 77 MET cc_start: 0.0892 (OUTLIER) cc_final: 0.0247 (tpp) REVERT: G 145 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5420 (ppp) REVERT: H 73 MET cc_start: -0.2492 (mmt) cc_final: -0.2816 (ttm) outliers start: 43 outliers final: 22 residues processed: 254 average time/residue: 2.0051 time to fit residues: 578.8326 Evaluate side-chains 232 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 HIS ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 15560 Z= 0.544 Angle : 0.620 7.538 20980 Z= 0.338 Chirality : 0.039 0.150 2296 Planarity : 0.004 0.043 2636 Dihedral : 6.909 42.655 2240 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.19 % Allowed : 27.41 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.19), residues: 1844 helix: 1.72 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.40 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 269 HIS 0.012 0.001 HIS H 108 PHE 0.014 0.002 PHE D 297 TYR 0.011 0.002 TYR D 237 ARG 0.006 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 215 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8731 (m-40) cc_final: 0.8512 (m-40) REVERT: C 123 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8015 (tm-30) REVERT: C 130 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7243 (tm-30) REVERT: D 130 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7450 (tm-30) REVERT: D 579 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7800 (tp) REVERT: E 73 MET cc_start: -0.2567 (mmt) cc_final: -0.3175 (ttm) REVERT: F 77 MET cc_start: 0.2440 (tpp) cc_final: 0.1850 (tpp) REVERT: F 141 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7570 (tm-30) REVERT: F 145 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6136 (ptt) REVERT: G 77 MET cc_start: 0.1537 (OUTLIER) cc_final: 0.1024 (tpp) REVERT: G 145 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.5421 (ppp) REVERT: H 73 MET cc_start: -0.2563 (mmt) cc_final: -0.2883 (ttm) REVERT: H 77 MET cc_start: 0.2831 (tpp) cc_final: 0.2489 (tpp) REVERT: H 110 MET cc_start: 0.7419 (mmm) cc_final: 0.7075 (mmm) outliers start: 66 outliers final: 42 residues processed: 262 average time/residue: 1.6249 time to fit residues: 496.5069 Evaluate side-chains 253 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 207 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 ASN ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15560 Z= 0.312 Angle : 0.537 8.511 20980 Z= 0.287 Chirality : 0.033 0.128 2296 Planarity : 0.003 0.036 2636 Dihedral : 6.343 43.878 2236 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.93 % Allowed : 28.11 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.19), residues: 1844 helix: 1.83 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 270 HIS 0.006 0.001 HIS H 108 PHE 0.014 0.001 PHE F 142 TYR 0.008 0.001 TYR B 118 ARG 0.006 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8793 (m-40) cc_final: 0.8326 (t0) REVERT: B 553 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8199 (tpp80) REVERT: C 123 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7951 (tm-30) REVERT: C 130 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 123 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7954 (tm-30) REVERT: D 130 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 334 ASN cc_start: 0.8815 (m-40) cc_final: 0.8586 (m110) REVERT: D 579 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7767 (tp) REVERT: E 73 MET cc_start: -0.2436 (mmt) cc_final: -0.3033 (ttm) REVERT: F 77 MET cc_start: 0.2399 (tpp) cc_final: 0.1848 (tpp) REVERT: F 141 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7572 (tm-30) REVERT: F 145 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6164 (ptt) REVERT: G 77 MET cc_start: 0.1530 (OUTLIER) cc_final: 0.0999 (tpp) REVERT: G 145 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.5575 (ppp) REVERT: H 73 MET cc_start: -0.2522 (mmt) cc_final: -0.2845 (ttm) REVERT: H 113 LEU cc_start: 0.7484 (tp) cc_final: 0.7037 (tp) outliers start: 62 outliers final: 39 residues processed: 257 average time/residue: 1.8559 time to fit residues: 548.3528 Evaluate side-chains 246 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 40.0000 chunk 20 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 40.0000 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15560 Z= 0.155 Angle : 0.499 10.515 20980 Z= 0.260 Chirality : 0.031 0.123 2296 Planarity : 0.003 0.075 2636 Dihedral : 5.174 39.869 2236 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.86 % Allowed : 29.31 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.20), residues: 1844 helix: 2.15 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.33 (0.37), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 288 HIS 0.002 0.000 HIS F 108 PHE 0.012 0.001 PHE A 297 TYR 0.011 0.001 TYR C 141 ARG 0.009 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 223 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8795 (m-40) cc_final: 0.8328 (t0) REVERT: B 553 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8282 (tpp80) REVERT: B 565 MET cc_start: 0.7181 (tpt) cc_final: 0.6965 (mmm) REVERT: C 123 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7933 (tm-30) REVERT: C 130 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 123 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7918 (tm-30) REVERT: D 130 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7373 (tm-30) REVERT: D 334 ASN cc_start: 0.8749 (m-40) cc_final: 0.8239 (t0) REVERT: E 73 MET cc_start: -0.2211 (mmt) cc_final: -0.2816 (ttm) REVERT: F 77 MET cc_start: 0.2362 (tpp) cc_final: 0.1811 (tpp) REVERT: F 141 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 145 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6170 (ptt) REVERT: G 77 MET cc_start: 0.1121 (tpp) cc_final: 0.0547 (tpp) REVERT: G 145 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.5445 (ppp) REVERT: H 73 MET cc_start: -0.2536 (mmt) cc_final: -0.2858 (ttm) REVERT: H 110 MET cc_start: 0.7437 (mmm) cc_final: 0.7148 (mmm) REVERT: H 113 LEU cc_start: 0.7588 (tp) cc_final: 0.7053 (tp) outliers start: 45 outliers final: 34 residues processed: 258 average time/residue: 1.8221 time to fit residues: 541.3856 Evaluate side-chains 248 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 161 optimal weight: 40.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15560 Z= 0.226 Angle : 0.519 10.339 20980 Z= 0.272 Chirality : 0.032 0.121 2296 Planarity : 0.003 0.064 2636 Dihedral : 5.302 43.304 2236 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.98 % Allowed : 28.93 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.20), residues: 1844 helix: 2.19 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -0.36 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 288 HIS 0.002 0.001 HIS H 108 PHE 0.017 0.001 PHE F 142 TYR 0.010 0.001 TYR A 141 ARG 0.009 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8768 (m-40) cc_final: 0.8315 (t0) REVERT: B 553 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8386 (tpp80) REVERT: C 130 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7252 (tm-30) REVERT: D 123 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7925 (tm-30) REVERT: D 130 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7397 (tm-30) REVERT: D 334 ASN cc_start: 0.8669 (m-40) cc_final: 0.8452 (m-40) REVERT: E 73 MET cc_start: -0.2194 (mmt) cc_final: -0.2748 (ttm) REVERT: F 141 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 145 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6181 (ptt) REVERT: G 77 MET cc_start: 0.1327 (tpp) cc_final: 0.0774 (tpp) REVERT: G 145 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.5487 (ppp) REVERT: H 73 MET cc_start: -0.2525 (mmt) cc_final: -0.2849 (ttm) REVERT: H 113 LEU cc_start: 0.7457 (tp) cc_final: 0.7079 (tp) outliers start: 47 outliers final: 37 residues processed: 257 average time/residue: 1.7277 time to fit residues: 515.0112 Evaluate side-chains 247 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 208 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 129 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 164 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15560 Z= 0.302 Angle : 0.554 10.723 20980 Z= 0.291 Chirality : 0.033 0.122 2296 Planarity : 0.003 0.061 2636 Dihedral : 5.705 46.691 2236 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.98 % Allowed : 29.44 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.20), residues: 1844 helix: 2.05 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 344 HIS 0.003 0.001 HIS D 228 PHE 0.019 0.001 PHE B 80 TYR 0.009 0.001 TYR D 127 ARG 0.009 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 209 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8749 (m-40) cc_final: 0.8301 (t0) REVERT: C 123 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7948 (tm-30) REVERT: C 130 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7238 (tm-30) REVERT: D 123 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7938 (tm-30) REVERT: D 130 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7420 (tm-30) REVERT: E 73 MET cc_start: -0.2257 (mmt) cc_final: -0.2772 (ttm) REVERT: F 141 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7566 (tm-30) REVERT: F 145 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.6230 (ptt) REVERT: G 77 MET cc_start: 0.1539 (tpp) cc_final: 0.0965 (tpp) REVERT: G 110 MET cc_start: 0.7265 (mmm) cc_final: 0.6775 (mmm) REVERT: G 145 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.5556 (ppp) REVERT: H 73 MET cc_start: -0.2505 (mmt) cc_final: -0.2856 (ttm) REVERT: H 110 MET cc_start: 0.7436 (mmm) cc_final: 0.6892 (mmm) outliers start: 47 outliers final: 40 residues processed: 247 average time/residue: 1.8117 time to fit residues: 516.2017 Evaluate side-chains 246 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 142 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15560 Z= 0.191 Angle : 0.523 11.122 20980 Z= 0.273 Chirality : 0.032 0.122 2296 Planarity : 0.003 0.060 2636 Dihedral : 5.240 45.349 2236 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.28 % Allowed : 29.82 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.20), residues: 1844 helix: 2.17 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -0.32 (0.37), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.003 0.001 HIS E 108 PHE 0.019 0.001 PHE F 142 TYR 0.018 0.001 TYR C 571 ARG 0.008 0.000 ARG F 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8752 (m-40) cc_final: 0.8315 (t0) REVERT: C 130 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7262 (tm-30) REVERT: D 130 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7423 (tm-30) REVERT: D 334 ASN cc_start: 0.8830 (m-40) cc_final: 0.8412 (t0) REVERT: E 73 MET cc_start: -0.2241 (mmt) cc_final: -0.2731 (ttm) REVERT: F 110 MET cc_start: 0.7411 (mmm) cc_final: 0.7121 (mmm) REVERT: F 141 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7560 (tm-30) REVERT: F 145 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6201 (ptt) REVERT: G 145 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5662 (ppp) REVERT: H 73 MET cc_start: -0.2522 (mmt) cc_final: -0.2869 (ttm) outliers start: 36 outliers final: 33 residues processed: 239 average time/residue: 1.7790 time to fit residues: 497.1374 Evaluate side-chains 242 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.179496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.105904 restraints weight = 70098.906| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.25 r_work: 0.3259 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15560 Z= 0.284 Angle : 0.550 11.183 20980 Z= 0.290 Chirality : 0.033 0.120 2296 Planarity : 0.003 0.026 2636 Dihedral : 5.562 48.131 2236 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.41 % Allowed : 29.82 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.20), residues: 1844 helix: 2.06 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.003 0.001 HIS D 228 PHE 0.017 0.001 PHE B 80 TYR 0.017 0.001 TYR B 571 ARG 0.005 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10225.23 seconds wall clock time: 180 minutes 8.10 seconds (10808.10 seconds total)