Starting phenix.real_space_refine on Fri Dec 15 06:59:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/12_2023/8j03_35882_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/12_2023/8j03_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_35882/12_2023/8j03_35882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/12_2023/8j03_35882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/12_2023/8j03_35882_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j03_35882/12_2023/8j03_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-1.21rc1-5172/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: 13.16, per 1000 atoms: 0.43 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: 27.48 Conformation dependent library (CDL) restraints added in 3.1 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: 4.64 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: 10.91 Time building geometry restraints manager: 28.13 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: 12545 21.25 - 42.51: 1081 42.51 - 63.76: 215 63.76 - 85.01: 35 85.01 - 106.27: 16 Dihedral angle restraints: 13892 sinusoidal: 7256 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 13889 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.460 Extract box with map and model: 4.660 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 97.690 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.100 ------------------------------------------------------------------------------- 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 : 2.672 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 outliers start: 36 outliers final: 17 residues processed: 223 average time/residue: 1.9375 time to fit residues: 495.8311 Evaluate side-chains 171 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 4 average time/residue: 0.3633 time to fit residues: 5.6852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 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: 9.9990 chunk 109 optimal weight: 0.2980 chunk 170 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15544 Z= 0.178 Angle : 0.495 6.588 20952 Z= 0.265 Chirality : 0.032 0.117 2308 Planarity : 0.004 0.037 2636 Dihedral : 7.097 48.414 2160 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.41 % Allowed : 27.34 % 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: 1.26 (0.20), residues: 1860 helix: 1.23 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 344 HIS 0.002 0.000 HIS J 108 PHE 0.009 0.001 PHE I 297 TYR 0.009 0.001 TYR I 237 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 222 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 168 time to evaluate : 2.357 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 outliers start: 54 outliers final: 26 residues processed: 203 average time/residue: 1.6809 time to fit residues: 400.9610 Evaluate side-chains 182 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 9 average time/residue: 0.5030 time to fit residues: 9.8650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 116 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 0.0980 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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: 0.6749 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15544 Z= 0.211 Angle : 0.480 6.452 20952 Z= 0.264 Chirality : 0.033 0.118 2308 Planarity : 0.004 0.041 2636 Dihedral : 6.031 39.438 2160 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.35 % Allowed : 26.58 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1860 helix: 1.27 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 344 HIS 0.003 0.001 HIS J 108 PHE 0.009 0.001 PHE G 329 TYR 0.010 0.001 TYR I 237 ARG 0.008 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 218 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 197 average time/residue: 1.6980 time to fit residues: 390.6512 Evaluate side-chains 182 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 9 average time/residue: 0.3439 time to fit residues: 8.2615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 162 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 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: 0.6809 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15544 Z= 0.384 Angle : 0.549 9.100 20952 Z= 0.303 Chirality : 0.037 0.138 2308 Planarity : 0.005 0.045 2636 Dihedral : 8.141 54.379 2160 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.80 % Allowed : 25.82 % Favored : 69.38 % 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: 0.72 (0.20), residues: 1860 helix: 0.86 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 344 HIS 0.006 0.001 HIS I 575 PHE 0.012 0.001 PHE G 329 TYR 0.013 0.001 TYR D 347 ARG 0.006 0.000 ARG J 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 231 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 155 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 34 residues processed: 210 average time/residue: 1.8728 time to fit residues: 453.3215 Evaluate side-chains 181 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 24 residues processed: 11 average time/residue: 0.8241 time to fit residues: 15.0902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 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** ** 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: 0.6800 moved from start: 0.2436 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= 0.325 Angle : 0.522 6.724 20952 Z= 0.290 Chirality : 0.035 0.128 2308 Planarity : 0.004 0.044 2636 Dihedral : 7.360 48.114 2160 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.17 % Allowed : 27.21 % 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: 0.65 (0.19), residues: 1860 helix: 0.82 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 344 HIS 0.004 0.001 HIS J 108 PHE 0.011 0.001 PHE G 329 TYR 0.008 0.001 TYR D 237 ARG 0.006 0.000 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 222 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 156 time to evaluate : 3.451 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 outliers start: 66 outliers final: 41 residues processed: 204 average time/residue: 1.8323 time to fit residues: 432.9166 Evaluate side-chains 187 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 13 average time/residue: 0.8535 time to fit residues: 16.5537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 181 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- 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** E 98 ASN H 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15544 Z= 0.151 Angle : 0.479 6.130 20952 Z= 0.261 Chirality : 0.032 0.114 2308 Planarity : 0.004 0.038 2636 Dihedral : 5.623 37.396 2160 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.41 % Allowed : 28.03 % Favored : 68.56 % 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: 1.18 (0.20), residues: 1860 helix: 1.18 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -0.48 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 344 HIS 0.002 0.001 HIS I 575 PHE 0.010 0.001 PHE G 297 TYR 0.013 0.001 TYR G 127 ARG 0.004 0.000 ARG J 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 206 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 2.532 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 outliers start: 54 outliers final: 32 residues processed: 191 average time/residue: 1.7090 time to fit residues: 378.4348 Evaluate side-chains 178 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 7 average time/residue: 0.4784 time to fit residues: 7.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** ** 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: 0.6766 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15544 Z= 0.198 Angle : 0.483 6.047 20952 Z= 0.265 Chirality : 0.033 0.116 2308 Planarity : 0.004 0.044 2636 Dihedral : 5.597 36.458 2160 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.16 % Allowed : 28.22 % 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: 1.23 (0.20), residues: 1860 helix: 1.19 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 344 HIS 0.003 0.001 HIS I 575 PHE 0.009 0.001 PHE I 329 TYR 0.009 0.001 TYR G 127 ARG 0.006 0.000 ARG A 201 *********************** 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 202 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 32 residues processed: 189 average time/residue: 1.7801 time to fit residues: 393.1857 Evaluate side-chains 183 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 2.432 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 7 average time/residue: 0.6026 time to fit residues: 9.3079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.2695 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: