Starting phenix.real_space_refine on Thu Mar 21 16:55:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/03_2024/8j03_35882_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/03_2024/8j03_35882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/03_2024/8j03_35882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/03_2024/8j03_35882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/03_2024/8j03_35882_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/03_2024/8j03_35882_neut_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 9848 2.51 5 N 2576 2.21 5 O 2720 1.98 5 H 15084 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 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 231": "OE1" <-> "OE2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 172": "OD1" <-> "OD2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30316 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} 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: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} 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: "G" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} 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: "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: "I" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} 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: "J" 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: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.22, per 1000 atoms: 0.44 Number of scatterers: 30316 At special positions: 0 Unit cell: (123.69, 122.76, 119.04, 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 2720 8.00 N 2576 7.00 C 9848 6.00 H 15084 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: 24.09 Conformation dependent library (CDL) restraints added in 2.8 seconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 0 sheets defined 75.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 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: 3.790A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.574A 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 211 removed outlier: 4.153A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) 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: 3.987A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.618A 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 333 through 347 Processing helix chain 'A' and resid 536 through 559 Processing helix chain 'A' and resid 564 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: 3.795A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.510A 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 211 removed outlier: 4.167A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 254 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 326 removed outlier: 3.978A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 333 through 347 Processing helix chain 'D' and resid 536 through 559 Processing helix chain 'D' and resid 564 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 74 Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.922A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 91 through 114 Processing helix chain 'G' and resid 119 through 150 removed outlier: 3.795A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N CYS G 150 " --> pdb=" O TRP G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 197 through 211 removed outlier: 4.159A pdb=" N MET G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 229 through 254 Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 288 through 326 removed outlier: 3.979A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix Processing helix chain 'G' and resid 333 through 347 Processing helix chain 'G' and resid 536 through 559 Processing helix chain 'G' and resid 564 through 594 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 removed outlier: 3.984A pdb=" N THR H 111 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN H 112 " --> pdb=" O HIS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 140 through 147 Processing helix chain 'I' and resid 71 through 85 Processing helix chain 'I' and resid 91 through 114 Processing helix chain 'I' and resid 119 through 150 removed outlier: 3.796A pdb=" N ILE I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY I 149 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N CYS I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 164 Processing helix chain 'I' and resid 167 through 183 Processing helix chain 'I' and resid 197 through 211 removed outlier: 4.181A pdb=" N MET I 211 " --> pdb=" O ARG I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 227 Processing helix chain 'I' and resid 229 through 254 Processing helix chain 'I' and resid 264 through 275 Processing helix chain 'I' and resid 288 through 326 removed outlier: 3.925A pdb=" N ILE I 300 " --> pdb=" O THR I 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) Proline residue: I 308 - end of helix Processing helix chain 'I' and resid 333 through 347 Processing helix chain 'I' and resid 536 through 559 Processing helix chain 'I' and resid 564 through 594 Processing helix chain 'J' and resid 7 through 20 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 46 through 56 Processing helix chain 'J' and resid 66 through 73 Processing helix chain 'J' and resid 83 through 93 Processing helix chain 'J' and resid 103 through 112 removed outlier: 3.877A pdb=" N THR J 111 " --> pdb=" O ARG J 107 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN J 112 " --> pdb=" O HIS J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 129 Processing helix chain 'J' and resid 140 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 removed outlier: 3.990A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 140 through 147 1048 hydrogen bonds defined for protein. 2556 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: 25.15 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: 15056 1.03 - 1.23: 50 1.23 - 1.42: 6630 1.42 - 1.62: 8736 1.62 - 1.81: 156 Bond restraints: 30628 Sorted by residual: bond pdb=" C07 P0T D 801 " pdb=" C09 P0T D 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C07 P0T I 801 " pdb=" C09 P0T I 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C07 P0T G 801 " pdb=" C09 P0T G 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C07 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C10 P0T I 801 " pdb=" C19 P0T I 801 " ideal model delta sigma weight residual 1.331 1.550 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 30623 not shown) Histogram of bond angle deviations from ideal: 81.27 - 91.82: 4 91.82 - 102.36: 56 102.36 - 112.90: 35009 112.90 - 123.44: 17551 123.44 - 133.98: 2500 Bond angle restraints: 55120 Sorted by residual: angle pdb=" C07 P0T I 801 " pdb=" C04 P0T I 801 " pdb=" C08 P0T I 801 " ideal model delta sigma weight residual 112.03 81.27 30.76 3.00e+00 1.11e-01 1.05e+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 81.28 30.75 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C07 P0T G 801 " pdb=" C04 P0T G 801 " pdb=" C08 P0T G 801 " ideal model delta sigma weight residual 112.03 81.32 30.71 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C07 P0T D 801 " pdb=" C04 P0T D 801 " pdb=" C08 P0T D 801 " ideal model delta sigma weight residual 112.03 81.33 30.70 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C03 P0T G 801 " pdb=" C04 P0T G 801 " pdb=" C08 P0T G 801 " ideal model delta sigma weight residual 111.12 130.77 -19.65 3.00e+00 1.11e-01 4.29e+01 ... (remaining 55115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 12740 21.25 - 42.51: 1128 42.51 - 63.76: 377 63.76 - 85.01: 35 85.01 - 106.27: 16 Dihedral angle restraints: 14296 sinusoidal: 7660 harmonic: 6636 Sorted by residual: dihedral pdb=" C03 P0T I 801 " pdb=" C05 P0T I 801 " pdb=" C06 P0T I 801 " pdb=" C09 P0T I 801 " ideal model delta sinusoidal sigma weight residual 49.00 -57.27 106.27 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C03 P0T A 801 " pdb=" C05 P0T A 801 " pdb=" C06 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sinusoidal sigma weight residual 49.00 -57.26 106.26 1 3.00e+01 1.11e-03 1.37e+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 -57.16 106.16 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 14293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1564 0.027 - 0.054: 455 0.054 - 0.080: 202 0.080 - 0.107: 73 0.107 - 0.134: 14 Chirality restraints: 2308 Sorted by residual: chirality pdb=" CB ILE D 134 " pdb=" CA ILE D 134 " pdb=" CG1 ILE D 134 " pdb=" CG2 ILE D 134 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB ILE I 134 " pdb=" CA ILE I 134 " pdb=" CG1 ILE I 134 " pdb=" CG2 ILE I 134 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CB ILE G 134 " pdb=" CA ILE G 134 " pdb=" CG1 ILE G 134 " pdb=" CG2 ILE G 134 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 2305 not shown) Planarity restraints: 4480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 579 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LEU D 579 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU D 579 " 0.011 2.00e-02 2.50e+03 pdb=" N SER D 580 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 579 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LEU I 579 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU I 579 " -0.011 2.00e-02 2.50e+03 pdb=" N SER I 580 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 560 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO D 561 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " 0.021 5.00e-02 4.00e+02 ... (remaining 4477 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1704 2.16 - 2.77: 59515 2.77 - 3.38: 89094 3.38 - 3.99: 106768 3.99 - 4.60: 168887 Nonbonded interactions: 425968 Sorted by model distance: nonbonded pdb=" OE1 GLU I 231 " pdb=" H GLU I 231 " model vdw 1.552 1.850 nonbonded pdb=" OE1 GLU G 231 " pdb=" H GLU G 231 " model vdw 1.552 1.850 nonbonded pdb="HE21 GLN I 341 " pdb=" O GLU J 115 " model vdw 1.582 1.850 nonbonded pdb="HE21 GLN D 341 " pdb=" O GLU E 115 " model vdw 1.583 1.850 nonbonded pdb="HE21 GLN G 341 " pdb=" O GLU H 115 " model vdw 1.585 1.850 ... (remaining 425963 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 'D' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' } 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: 0.610 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: 0.430 Extract box with map and model: 4.650 Check model and map are aligned: 0.460 Set scattering table: 0.250 Process input model: 93.620 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 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 : 0.008 0.258 15544 Z= 0.557 Angle : 0.754 30.757 20952 Z= 0.339 Chirality : 0.034 0.134 2308 Planarity : 0.004 0.040 2636 Dihedral : 18.805 106.267 5704 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.27 % Allowed : 29.29 % Favored : 68.43 % 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: 1.00 (0.20), residues: 1860 helix: 1.01 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.003 0.001 HIS J 108 PHE 0.010 0.001 PHE I 297 TYR 0.016 0.001 TYR A 127 ARG 0.005 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 230 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 2.371 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: D 163 PHE cc_start: 0.8389 (t80) cc_final: 0.8177 (t80) REVERT: D 211 MET cc_start: 0.8766 (tpp) cc_final: 0.8537 (ttt) REVERT: E 145 MET cc_start: 0.3327 (pp-130) cc_final: 0.2780 (tmm) REVERT: E 146 MET cc_start: 0.4532 (tpp) cc_final: 0.4087 (tpp) REVERT: G 229 SER cc_start: 0.8843 (t) cc_final: 0.8522 (p) REVERT: G 575 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.7027 (t-170) REVERT: I 226 TYR cc_start: 0.8535 (t80) cc_final: 0.8225 (t80) REVERT: I 229 SER cc_start: 0.8457 (t) cc_final: 0.8138 (p) REVERT: F 37 MET cc_start: 0.0731 (ttm) cc_final: 0.0498 (ttm) REVERT: F 77 MET cc_start: -0.0417 (mtt) cc_final: -0.0621 (mtt) REVERT: F 92 VAL cc_start: 0.6042 (t) cc_final: 0.5704 (t) REVERT: F 140 GLU cc_start: 0.7186 (mp0) cc_final: 0.6241 (tp30) REVERT: F 145 MET cc_start: 0.2536 (OUTLIER) cc_final: 0.2193 (tmm) outliers start: 36 outliers final: 17 residues processed: 223 average time/residue: 1.9272 time to fit residues: 492.4064 Evaluate side-chains 179 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 0.0570 chunk 170 optimal weight: 0.6980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15544 Z= 0.157 Angle : 0.488 5.949 20952 Z= 0.260 Chirality : 0.032 0.117 2308 Planarity : 0.004 0.037 2636 Dihedral : 7.769 46.875 2191 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.65 % Allowed : 28.09 % Favored : 69.26 % 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: 1.32 (0.20), residues: 1860 helix: 1.26 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.38 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 344 HIS 0.001 0.000 HIS J 108 PHE 0.009 0.001 PHE G 346 TYR 0.009 0.001 TYR A 127 ARG 0.006 0.000 ARG I 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 215 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 2.404 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: A 546 MET cc_start: 0.2228 (mmt) cc_final: 0.1938 (mtp) REVERT: D 163 PHE cc_start: 0.8375 (t80) cc_final: 0.8116 (t80) REVERT: E 145 MET cc_start: 0.3194 (OUTLIER) cc_final: 0.2697 (tmm) REVERT: E 146 MET cc_start: 0.4560 (tpp) cc_final: 0.4289 (tpt) REVERT: G 134 ILE cc_start: 0.8355 (pp) cc_final: 0.8102 (pp) REVERT: G 229 SER cc_start: 0.8946 (t) cc_final: 0.8653 (t) REVERT: H 146 MET cc_start: 0.3569 (tpp) cc_final: 0.3332 (tpp) REVERT: I 226 TYR cc_start: 0.8586 (t80) cc_final: 0.8156 (t80) REVERT: I 229 SER cc_start: 0.8619 (t) cc_final: 0.8105 (m) REVERT: F 140 GLU cc_start: 0.7166 (mp0) cc_final: 0.6251 (tp30) REVERT: F 145 MET cc_start: 0.2729 (pp-130) cc_final: 0.2453 (tmm) outliers start: 42 outliers final: 19 residues processed: 196 average time/residue: 1.7879 time to fit residues: 406.6508 Evaluate side-chains 181 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 334 ASN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15544 Z= 0.201 Angle : 0.475 5.238 20952 Z= 0.262 Chirality : 0.032 0.118 2308 Planarity : 0.004 0.041 2636 Dihedral : 6.417 45.738 2176 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.22 % Allowed : 26.64 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1860 helix: 1.32 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.40 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.002 0.001 HIS J 108 PHE 0.009 0.001 PHE G 329 TYR 0.010 0.001 TYR I 237 ARG 0.007 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 221 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 170 time to evaluate : 2.373 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: A 226 TYR cc_start: 0.8805 (t80) cc_final: 0.8540 (t80) REVERT: A 546 MET cc_start: 0.2738 (mmt) cc_final: 0.2422 (mtp) REVERT: D 163 PHE cc_start: 0.8381 (t80) cc_final: 0.8136 (t80) REVERT: D 211 MET cc_start: 0.8823 (tpp) cc_final: 0.8535 (ttt) REVERT: E 145 MET cc_start: 0.3313 (OUTLIER) cc_final: 0.2806 (tmm) REVERT: E 146 MET cc_start: 0.4497 (tpp) cc_final: 0.4256 (tpt) REVERT: H 87 ARG cc_start: 0.5275 (mmp80) cc_final: 0.4586 (mmp80) REVERT: I 134 ILE cc_start: 0.8157 (pp) cc_final: 0.7873 (pp) REVERT: J 32 GLU cc_start: 0.6863 (mp0) cc_final: 0.6626 (mp0) REVERT: F 140 GLU cc_start: 0.7198 (mp0) cc_final: 0.6291 (tp30) REVERT: F 145 MET cc_start: 0.2923 (OUTLIER) cc_final: 0.2557 (tmm) outliers start: 51 outliers final: 21 residues processed: 201 average time/residue: 1.6651 time to fit residues: 391.0723 Evaluate side-chains 182 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 334 ASN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.0060 chunk 128 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15544 Z= 0.309 Angle : 0.515 7.935 20952 Z= 0.284 Chirality : 0.035 0.130 2308 Planarity : 0.004 0.041 2636 Dihedral : 7.663 49.235 2172 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.91 % Allowed : 26.07 % Favored : 70.01 % 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: 1.03 (0.20), residues: 1860 helix: 1.07 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 344 HIS 0.004 0.001 HIS J 108 PHE 0.012 0.001 PHE G 137 TYR 0.008 0.001 TYR I 237 ARG 0.005 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 222 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 160 time to evaluate : 2.414 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: A 546 MET cc_start: 0.2731 (mmt) cc_final: 0.2481 (mtp) REVERT: A 557 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: D 163 PHE cc_start: 0.8404 (t80) cc_final: 0.8177 (t80) REVERT: D 211 MET cc_start: 0.8970 (tpp) cc_final: 0.8715 (ttt) REVERT: D 557 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: E 37 MET cc_start: 0.0987 (tmm) cc_final: 0.0507 (tmm) REVERT: E 145 MET cc_start: 0.3448 (OUTLIER) cc_final: 0.2971 (tmm) REVERT: E 146 MET cc_start: 0.4490 (tpp) cc_final: 0.4277 (tpt) REVERT: G 557 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: I 557 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7665 (pp20) REVERT: F 73 MET cc_start: 0.0911 (pmm) cc_final: -0.0581 (ttm) REVERT: F 145 MET cc_start: 0.3427 (OUTLIER) cc_final: 0.3071 (tmm) outliers start: 62 outliers final: 28 residues processed: 203 average time/residue: 1.7709 time to fit residues: 416.6388 Evaluate side-chains 186 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 334 ASN Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 557 GLU Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 15544 Z= 0.487 Angle : 0.588 6.909 20952 Z= 0.327 Chirality : 0.040 0.152 2308 Planarity : 0.005 0.047 2636 Dihedral : 8.498 53.816 2172 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.80 % Allowed : 26.58 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1860 helix: 0.62 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.79 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 344 HIS 0.007 0.001 HIS J 108 PHE 0.014 0.002 PHE G 329 TYR 0.009 0.001 TYR G 237 ARG 0.015 0.001 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 232 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 156 time to evaluate : 2.481 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: A 546 MET cc_start: 0.2981 (mmt) cc_final: 0.2726 (mtp) REVERT: A 557 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: D 211 MET cc_start: 0.8984 (tpp) cc_final: 0.8783 (ttt) REVERT: D 557 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: E 86 ILE cc_start: 0.5483 (mt) cc_final: 0.5262 (mm) REVERT: H 87 ARG cc_start: 0.5555 (mmp80) cc_final: 0.5055 (mmp80) REVERT: F 145 MET cc_start: 0.3693 (OUTLIER) cc_final: 0.3429 (tmm) outliers start: 76 outliers final: 40 residues processed: 206 average time/residue: 1.9073 time to fit residues: 448.8964 Evaluate side-chains 188 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 20.0000 chunk 163 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 150 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15544 Z= 0.168 Angle : 0.487 5.732 20952 Z= 0.266 Chirality : 0.033 0.115 2308 Planarity : 0.004 0.039 2636 Dihedral : 6.869 50.940 2172 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.84 % Allowed : 28.66 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1860 helix: 0.95 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.002 0.001 HIS D 575 PHE 0.009 0.001 PHE G 329 TYR 0.011 0.001 TYR G 127 ARG 0.007 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 198 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 2.326 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: A 546 MET cc_start: 0.2977 (mmt) cc_final: 0.2722 (mtp) REVERT: E 86 ILE cc_start: 0.5478 (mt) cc_final: 0.5255 (mm) REVERT: E 145 MET cc_start: 0.3595 (OUTLIER) cc_final: 0.3237 (tmm) REVERT: G 557 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: F 73 MET cc_start: 0.1033 (pmm) cc_final: -0.0460 (ttm) REVERT: F 145 MET cc_start: 0.3413 (OUTLIER) cc_final: 0.3135 (tmm) outliers start: 45 outliers final: 26 residues processed: 184 average time/residue: 1.8815 time to fit residues: 398.7312 Evaluate side-chains 173 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15544 Z= 0.181 Angle : 0.478 6.014 20952 Z= 0.261 Chirality : 0.032 0.116 2308 Planarity : 0.004 0.038 2636 Dihedral : 6.015 51.068 2170 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.78 % Allowed : 28.91 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1860 helix: 1.13 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.002 0.000 HIS J 108 PHE 0.008 0.001 PHE G 329 TYR 0.009 0.001 TYR G 127 ARG 0.008 0.000 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 196 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 2.304 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: A 546 MET cc_start: 0.2960 (mmt) cc_final: 0.2727 (mtp) REVERT: E 145 MET cc_start: 0.3510 (OUTLIER) cc_final: 0.3229 (tmm) REVERT: G 557 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: F 73 MET cc_start: 0.1073 (pmm) cc_final: -0.0509 (ttm) REVERT: F 145 MET cc_start: 0.3502 (OUTLIER) cc_final: 0.3222 (tmm) outliers start: 44 outliers final: 22 residues processed: 183 average time/residue: 1.9343 time to fit residues: 405.8802 Evaluate side-chains 172 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15544 Z= 0.270 Angle : 0.509 6.824 20952 Z= 0.279 Chirality : 0.034 0.122 2308 Planarity : 0.004 0.037 2636 Dihedral : 6.606 50.900 2169 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.90 % Allowed : 28.91 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1860 helix: 1.03 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 344 HIS 0.005 0.001 HIS A 575 PHE 0.010 0.001 PHE I 240 TYR 0.007 0.001 TYR G 127 ARG 0.008 0.000 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 194 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 2.739 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: A 211 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8756 (ttt) REVERT: A 546 MET cc_start: 0.2975 (mmt) cc_final: 0.2748 (mtp) REVERT: A 557 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7566 (pp20) REVERT: D 557 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7502 (pp20) REVERT: E 37 MET cc_start: 0.1083 (tmm) cc_final: 0.0880 (tmm) REVERT: E 145 MET cc_start: 0.3810 (OUTLIER) cc_final: 0.3499 (tmm) REVERT: G 557 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7582 (pp20) REVERT: F 145 MET cc_start: 0.3492 (OUTLIER) cc_final: 0.3256 (tmm) outliers start: 46 outliers final: 31 residues processed: 177 average time/residue: 1.8666 time to fit residues: 383.4289 Evaluate side-chains 185 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 334 ASN Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15544 Z= 0.329 Angle : 0.532 6.720 20952 Z= 0.293 Chirality : 0.036 0.127 2308 Planarity : 0.004 0.041 2636 Dihedral : 6.910 50.986 2169 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.16 % Allowed : 28.79 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1860 helix: 0.89 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 344 HIS 0.008 0.001 HIS A 575 PHE 0.011 0.001 PHE G 329 TYR 0.007 0.001 TYR G 251 ARG 0.009 0.000 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 201 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 2.325 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: A 211 MET cc_start: 0.8964 (tpp) cc_final: 0.8701 (ttt) REVERT: A 546 MET cc_start: 0.2982 (mmt) cc_final: 0.2741 (mtp) REVERT: A 557 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: D 557 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: E 37 MET cc_start: 0.1184 (tmm) cc_final: 0.0982 (tmm) REVERT: G 557 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7603 (pp20) REVERT: F 73 MET cc_start: 0.0788 (pmm) cc_final: -0.0550 (ttm) outliers start: 50 outliers final: 33 residues processed: 184 average time/residue: 1.8847 time to fit residues: 399.4725 Evaluate side-chains 185 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15544 Z= 0.230 Angle : 0.508 6.749 20952 Z= 0.278 Chirality : 0.034 0.118 2308 Planarity : 0.004 0.041 2636 Dihedral : 6.262 51.952 2169 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.65 % Allowed : 29.23 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1860 helix: 0.97 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 344 HIS 0.002 0.001 HIS J 108 PHE 0.009 0.001 PHE G 240 TYR 0.007 0.001 TYR G 127 ARG 0.009 0.000 ARG J 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 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 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 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 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. Evaluate side-chains 189 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 2.409 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: A 211 MET cc_start: 0.8939 (tpp) cc_final: 0.8683 (ttt) REVERT: A 546 MET cc_start: 0.2981 (mmt) cc_final: 0.2749 (mtp) REVERT: D 557 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7518 (pp20) REVERT: E 37 MET cc_start: 0.1255 (tmm) cc_final: 0.1045 (tmm) REVERT: G 557 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7564 (pp20) REVERT: F 73 MET cc_start: 0.0786 (pmm) cc_final: -0.0601 (ttm) outliers start: 42 outliers final: 32 residues processed: 174 average time/residue: 1.9441 time to fit residues: 387.4889 Evaluate side-chains 180 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.226487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140953 restraints weight = 61293.096| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 5.59 r_work: 0.3362 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15544 Z= 0.202 Angle : 0.512 6.765 20952 Z= 0.278 Chirality : 0.033 0.140 2308 Planarity : 0.004 0.042 2636 Dihedral : 5.882 52.082 2169 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.78 % Allowed : 29.29 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1860 helix: 1.05 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -0.51 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 344 HIS 0.003 0.001 HIS A 575 PHE 0.009 0.001 PHE I 329 TYR 0.006 0.001 TYR D 237 ARG 0.008 0.000 ARG J 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8899.20 seconds wall clock time: 157 minutes 56.15 seconds (9476.15 seconds total)