Starting phenix.real_space_refine on Fri Mar 15 17:33:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/03_2024/6hjn_0234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/03_2024/6hjn_0234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/03_2024/6hjn_0234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/03_2024/6hjn_0234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/03_2024/6hjn_0234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/03_2024/6hjn_0234_updated.pdb" } resolution = 3.3 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= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7701 2.51 5 N 2031 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12309 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "B" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1395 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "D" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1395 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "F" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1395 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "E" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 17, 'TRANS': 305} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.61, per 1000 atoms: 0.54 Number of scatterers: 12309 At special positions: 0 Unit cell: (92.708, 91.63, 150.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2526 8.00 N 2031 7.00 C 7701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS C 8 " distance=2.05 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS E 8 " distance=2.05 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.02 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 3 " " NAG S 1 " - " FUC S 3 " NAG-ASN " NAG G 1 " - " ASN A 15 " " NAG H 1 " - " ASN A 27 " " NAG I 1 " - " ASN A 91 " " NAG J 1 " - " ASN A 290 " " NAG K 1 " - " ASN B 154 " " NAG L 1 " - " ASN D 154 " " NAG M 1 " - " ASN F 154 " " NAG N 1 " - " ASN C 15 " " NAG O 1 " - " ASN C 27 " " NAG P 1 " - " ASN C 91 " " NAG Q 1 " - " ASN C 290 " " NAG R 1 " - " ASN E 15 " " NAG S 1 " - " ASN E 27 " " NAG T 1 " - " ASN E 91 " " NAG U 1 " - " ASN E 290 " Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 23.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 49 through 50 No H-bonds generated for 'chain 'A' and resid 49 through 50' Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 102 through 111 removed outlier: 4.535A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'B' and resid 40 through 58 removed outlier: 3.695A pdb=" N ALA B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 125 removed outlier: 3.671A pdb=" N GLN B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'D' and resid 40 through 58 removed outlier: 3.695A pdb=" N ALA D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 125 removed outlier: 3.669A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'F' and resid 40 through 58 removed outlier: 3.695A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 125 removed outlier: 3.671A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'C' and resid 49 through 50 No H-bonds generated for 'chain 'C' and resid 49 through 50' Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 102 through 111 removed outlier: 4.535A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'E' and resid 49 through 50 No H-bonds generated for 'chain 'E' and resid 49 through 50' Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 102 through 111 removed outlier: 4.535A pdb=" N SER E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 194 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.855A pdb=" N MET A 230 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.132A pdb=" N SER A 114 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 261 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 118 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 164 through 168 Processing sheet with id= D, first strand: chain 'A' and resid 282 through 284 Processing sheet with id= E, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.855A pdb=" N MET C 230 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 114 through 118 removed outlier: 4.132A pdb=" N SER C 114 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 261 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 118 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 164 through 168 Processing sheet with id= H, first strand: chain 'C' and resid 282 through 284 Processing sheet with id= I, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.854A pdb=" N MET E 230 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 114 through 118 removed outlier: 4.132A pdb=" N SER E 114 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN E 261 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E 118 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 164 through 168 Processing sheet with id= L, first strand: chain 'E' and resid 282 through 284 324 hydrogen bonds defined for protein. 927 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: 2.82 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3736 1.33 - 1.45: 2147 1.45 - 1.57: 6627 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 12576 Sorted by residual: bond pdb=" N ASN A 290 " pdb=" CA ASN A 290 " ideal model delta sigma weight residual 1.460 1.405 0.055 1.17e-02 7.31e+03 2.20e+01 bond pdb=" N ASN E 290 " pdb=" CA ASN E 290 " ideal model delta sigma weight residual 1.460 1.406 0.054 1.17e-02 7.31e+03 2.16e+01 bond pdb=" N ASN C 290 " pdb=" CA ASN C 290 " ideal model delta sigma weight residual 1.460 1.406 0.054 1.17e-02 7.31e+03 2.15e+01 bond pdb=" N LYS F 131 " pdb=" CA LYS F 131 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.47e+00 bond pdb=" N LYS B 131 " pdb=" CA LYS B 131 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.43e+00 ... (remaining 12571 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.77: 278 105.77 - 112.88: 6505 112.88 - 119.99: 4638 119.99 - 127.10: 5451 127.10 - 134.21: 177 Bond angle restraints: 17049 Sorted by residual: angle pdb=" CA ASP F 158 " pdb=" CB ASP F 158 " pdb=" CG ASP F 158 " ideal model delta sigma weight residual 112.60 118.11 -5.51 1.00e+00 1.00e+00 3.03e+01 angle pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " pdb=" CG ASP B 158 " ideal model delta sigma weight residual 112.60 117.77 -5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " pdb=" CG ASP D 158 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" C ASP F 158 " pdb=" N TYR F 159 " pdb=" CA TYR F 159 " ideal model delta sigma weight residual 120.58 126.39 -5.81 1.32e+00 5.74e-01 1.94e+01 angle pdb=" C ASP B 158 " pdb=" N TYR B 159 " pdb=" CA TYR B 159 " ideal model delta sigma weight residual 120.58 126.36 -5.78 1.32e+00 5.74e-01 1.92e+01 ... (remaining 17044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.72: 7529 20.72 - 41.44: 385 41.44 - 62.16: 72 62.16 - 82.88: 42 82.88 - 103.60: 24 Dihedral angle restraints: 8052 sinusoidal: 3756 harmonic: 4296 Sorted by residual: dihedral pdb=" C ASP D 158 " pdb=" N ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta harmonic sigma weight residual -122.60 -136.75 14.15 0 2.50e+00 1.60e-01 3.20e+01 dihedral pdb=" C ASP B 158 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta harmonic sigma weight residual -122.60 -136.61 14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA ASN B 129 " pdb=" C ASN B 129 " pdb=" N ALA B 130 " pdb=" CA ALA B 130 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 8049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 1953 0.287 - 0.574: 9 0.574 - 0.860: 3 0.860 - 1.147: 3 1.147 - 1.434: 3 Chirality restraints: 1971 Sorted by residual: chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.90e+03 chirality pdb=" C1 MAN I 4 " pdb=" O3 BMA I 3 " pdb=" C2 MAN I 4 " pdb=" O5 MAN I 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.89e+03 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 1.53 0.87 2.00e-02 2.50e+03 1.89e+03 ... (remaining 1968 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG G 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.513 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG N 2 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.086 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG R 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.512 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.165 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 18 2.37 - 3.00: 6105 3.00 - 3.63: 17446 3.63 - 4.27: 25932 4.27 - 4.90: 43224 Nonbonded interactions: 92725 Sorted by model distance: nonbonded pdb=" CE2 TYR C 161 " pdb=" O THR C 248 " model vdw 1.734 3.340 nonbonded pdb=" CE2 TYR E 161 " pdb=" O THR E 248 " model vdw 1.735 3.340 nonbonded pdb=" CE2 TYR A 161 " pdb=" O THR A 248 " model vdw 1.735 3.340 nonbonded pdb=" OD1 ASN D 128 " pdb=" NH1 ARG D 170 " model vdw 2.051 2.520 nonbonded pdb=" OD1 ASN F 128 " pdb=" NH1 ARG F 170 " model vdw 2.051 2.520 ... (remaining 92720 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } 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: 6.870 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: 0.030 Extract box with map and model: 29.350 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 33.020 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 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 0.057 12576 Z= 0.527 Angle : 1.231 11.639 17049 Z= 0.698 Chirality : 0.111 1.434 1971 Planarity : 0.022 0.287 2148 Dihedral : 15.251 103.604 5256 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.80 % Allowed : 4.44 % Favored : 92.76 % Cbeta Deviations : 0.22 % 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: -3.22 (0.17), residues: 1476 helix: -0.02 (0.24), residues: 351 sheet: -2.26 (0.28), residues: 258 loop : -3.19 (0.15), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP C 153 HIS 0.004 0.002 HIS C 276 PHE 0.013 0.003 PHE B 140 TYR 0.016 0.003 TYR D 157 ARG 0.007 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8801 (tm-30) REVERT: B 59 MET cc_start: 0.8838 (mmm) cc_final: 0.8537 (mmm) REVERT: B 149 MET cc_start: 0.9351 (mmt) cc_final: 0.9131 (mmp) REVERT: D 59 MET cc_start: 0.8923 (mmm) cc_final: 0.8621 (mmm) REVERT: D 149 MET cc_start: 0.9385 (mmt) cc_final: 0.9147 (mmp) REVERT: F 59 MET cc_start: 0.8823 (mmm) cc_final: 0.8554 (mmm) REVERT: F 149 MET cc_start: 0.9361 (mmt) cc_final: 0.9147 (mmp) REVERT: C 192 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8800 (tm-30) outliers start: 36 outliers final: 6 residues processed: 147 average time/residue: 0.3295 time to fit residues: 64.6482 Evaluate side-chains 64 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 286 HIS A 299 HIS ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 25 HIS ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN C 184 HIS C 286 HIS C 299 HIS E 184 HIS E 286 HIS E 299 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12576 Z= 0.281 Angle : 0.750 11.502 17049 Z= 0.349 Chirality : 0.050 0.417 1971 Planarity : 0.004 0.032 2148 Dihedral : 13.632 81.750 2550 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.57 % Allowed : 7.79 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1476 helix: 1.72 (0.27), residues: 351 sheet: -1.38 (0.32), residues: 219 loop : -3.01 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 255 HIS 0.003 0.001 HIS A 276 PHE 0.012 0.001 PHE B 9 TYR 0.016 0.001 TYR A 161 ARG 0.005 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 68 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8751 (tm-30) REVERT: B 59 MET cc_start: 0.8779 (mmm) cc_final: 0.8395 (mmm) REVERT: D 59 MET cc_start: 0.8895 (mmm) cc_final: 0.8603 (mmm) REVERT: D 149 MET cc_start: 0.9405 (mmt) cc_final: 0.9132 (mmp) REVERT: F 59 MET cc_start: 0.8778 (mmm) cc_final: 0.8493 (mmm) REVERT: F 149 MET cc_start: 0.9402 (mmt) cc_final: 0.9176 (mmp) REVERT: C 192 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8783 (tm-30) outliers start: 33 outliers final: 14 residues processed: 94 average time/residue: 0.3287 time to fit residues: 41.6702 Evaluate side-chains 71 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12576 Z= 0.256 Angle : 0.654 9.625 17049 Z= 0.314 Chirality : 0.046 0.284 1971 Planarity : 0.003 0.030 2148 Dihedral : 11.291 69.176 2546 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.65 % Allowed : 9.27 % Favored : 88.08 % 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: -1.48 (0.21), residues: 1476 helix: 2.63 (0.28), residues: 351 sheet: -0.86 (0.33), residues: 219 loop : -2.72 (0.17), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 92 HIS 0.004 0.001 HIS A 276 PHE 0.012 0.001 PHE D 9 TYR 0.013 0.001 TYR C 195 ARG 0.005 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 65 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8761 (tm-30) REVERT: B 59 MET cc_start: 0.8786 (mmm) cc_final: 0.8562 (mmm) REVERT: B 98 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9061 (tm) REVERT: D 59 MET cc_start: 0.8848 (mmm) cc_final: 0.8643 (mmm) REVERT: D 149 MET cc_start: 0.9432 (mmt) cc_final: 0.9217 (mmp) REVERT: F 2 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8814 (tm) REVERT: F 59 MET cc_start: 0.8772 (mmm) cc_final: 0.8511 (mmm) REVERT: C 115 PHE cc_start: 0.8270 (m-10) cc_final: 0.7998 (m-10) outliers start: 34 outliers final: 11 residues processed: 90 average time/residue: 0.2579 time to fit residues: 33.8523 Evaluate side-chains 66 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 0.0030 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12576 Z= 0.188 Angle : 0.618 9.610 17049 Z= 0.292 Chirality : 0.045 0.270 1971 Planarity : 0.003 0.028 2148 Dihedral : 10.433 59.380 2542 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.71 % Allowed : 10.51 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1476 helix: 2.98 (0.27), residues: 351 sheet: -0.50 (0.34), residues: 219 loop : -2.50 (0.17), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 92 HIS 0.003 0.001 HIS B 26 PHE 0.011 0.001 PHE B 9 TYR 0.013 0.001 TYR A 195 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8768 (tm-30) REVERT: B 27 GLN cc_start: 0.9324 (tp-100) cc_final: 0.9118 (tp-100) REVERT: B 59 MET cc_start: 0.8817 (mmm) cc_final: 0.8564 (mmm) REVERT: D 59 MET cc_start: 0.8853 (mmm) cc_final: 0.8628 (mmm) REVERT: F 2 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8774 (tm) REVERT: F 59 MET cc_start: 0.8742 (mmm) cc_final: 0.8501 (mmm) REVERT: E 115 PHE cc_start: 0.8258 (m-10) cc_final: 0.7980 (m-10) outliers start: 22 outliers final: 11 residues processed: 81 average time/residue: 0.2710 time to fit residues: 31.8724 Evaluate side-chains 61 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12576 Z= 0.258 Angle : 0.641 9.969 17049 Z= 0.304 Chirality : 0.045 0.255 1971 Planarity : 0.003 0.031 2148 Dihedral : 9.582 57.519 2542 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.73 % Allowed : 10.12 % Favored : 87.15 % 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: -0.83 (0.21), residues: 1476 helix: 3.18 (0.27), residues: 351 sheet: -0.20 (0.35), residues: 216 loop : -2.36 (0.17), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 92 HIS 0.004 0.001 HIS E 184 PHE 0.013 0.001 PHE D 9 TYR 0.011 0.001 TYR A 161 ARG 0.006 0.001 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 59 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.7892 (p90) REVERT: A 192 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8781 (tm-30) REVERT: B 27 GLN cc_start: 0.9326 (tp-100) cc_final: 0.9125 (tp-100) REVERT: B 59 MET cc_start: 0.8816 (mmm) cc_final: 0.8530 (mmm) REVERT: D 59 MET cc_start: 0.8902 (mmm) cc_final: 0.8629 (mmm) REVERT: F 2 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8715 (tm) REVERT: F 59 MET cc_start: 0.8808 (mmm) cc_final: 0.8520 (mmm) REVERT: E 115 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: E 184 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.6791 (p90) REVERT: E 196 GLN cc_start: 0.8353 (tt0) cc_final: 0.8118 (mt0) outliers start: 35 outliers final: 19 residues processed: 92 average time/residue: 0.2489 time to fit residues: 34.0040 Evaluate side-chains 77 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 142 optimal weight: 0.2980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12576 Z= 0.186 Angle : 0.619 11.171 17049 Z= 0.292 Chirality : 0.045 0.253 1971 Planarity : 0.003 0.028 2148 Dihedral : 8.581 56.880 2542 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.26 % Allowed : 10.51 % Favored : 87.23 % 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: -0.63 (0.22), residues: 1476 helix: 3.29 (0.27), residues: 351 sheet: -0.08 (0.35), residues: 219 loop : -2.22 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 92 HIS 0.005 0.001 HIS C 276 PHE 0.011 0.001 PHE D 9 TYR 0.009 0.001 TYR C 195 ARG 0.004 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 59 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.7887 (p90) REVERT: A 192 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8729 (tm-30) REVERT: B 27 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9141 (tp-100) REVERT: B 59 MET cc_start: 0.8819 (mmm) cc_final: 0.8527 (mmm) REVERT: D 59 MET cc_start: 0.8898 (mmm) cc_final: 0.8619 (mmm) REVERT: F 2 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8726 (tm) REVERT: F 59 MET cc_start: 0.8787 (mmm) cc_final: 0.8502 (mmm) REVERT: E 184 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.6826 (p90) REVERT: E 239 GLN cc_start: 0.9212 (mp10) cc_final: 0.8860 (mp10) outliers start: 29 outliers final: 19 residues processed: 86 average time/residue: 0.2605 time to fit residues: 32.8055 Evaluate side-chains 76 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS B 62 GLN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12576 Z= 0.187 Angle : 0.607 9.957 17049 Z= 0.286 Chirality : 0.044 0.246 1971 Planarity : 0.003 0.028 2148 Dihedral : 8.196 57.085 2542 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.95 % Allowed : 11.68 % Favored : 86.37 % 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: -0.46 (0.22), residues: 1476 helix: 3.48 (0.27), residues: 348 sheet: 0.09 (0.36), residues: 216 loop : -2.12 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 92 HIS 0.003 0.001 HIS E 276 PHE 0.013 0.001 PHE F 140 TYR 0.009 0.001 TYR E 195 ARG 0.003 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.7898 (p90) REVERT: B 27 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9136 (tp-100) REVERT: B 59 MET cc_start: 0.8816 (mmm) cc_final: 0.8527 (mmm) REVERT: D 59 MET cc_start: 0.8907 (mmm) cc_final: 0.8631 (mmm) REVERT: F 2 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8749 (tm) REVERT: F 59 MET cc_start: 0.8760 (mmm) cc_final: 0.8503 (mmm) REVERT: E 184 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.6716 (p90) outliers start: 25 outliers final: 16 residues processed: 81 average time/residue: 0.2511 time to fit residues: 30.4983 Evaluate side-chains 72 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.0030 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN E 32 HIS ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12576 Z= 0.268 Angle : 0.633 9.822 17049 Z= 0.301 Chirality : 0.044 0.242 1971 Planarity : 0.003 0.031 2148 Dihedral : 8.231 57.182 2542 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.79 % Allowed : 11.84 % Favored : 86.37 % 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: -0.41 (0.22), residues: 1476 helix: 3.40 (0.28), residues: 351 sheet: 0.21 (0.36), residues: 216 loop : -2.07 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 92 HIS 0.004 0.001 HIS C 276 PHE 0.013 0.001 PHE D 9 TYR 0.010 0.001 TYR E 102 ARG 0.004 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.7929 (p90) REVERT: B 27 GLN cc_start: 0.9357 (tp-100) cc_final: 0.9115 (tp-100) REVERT: B 59 MET cc_start: 0.8820 (mmm) cc_final: 0.8505 (mmm) REVERT: D 59 MET cc_start: 0.8883 (mmm) cc_final: 0.8610 (mmm) REVERT: F 2 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8829 (tm) REVERT: F 59 MET cc_start: 0.8764 (mmm) cc_final: 0.8479 (mmm) REVERT: E 184 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.6703 (p90) REVERT: E 239 GLN cc_start: 0.9173 (mp10) cc_final: 0.8890 (mp10) outliers start: 23 outliers final: 16 residues processed: 78 average time/residue: 0.2544 time to fit residues: 29.6169 Evaluate side-chains 73 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.0870 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12576 Z= 0.170 Angle : 0.601 9.609 17049 Z= 0.284 Chirality : 0.043 0.246 1971 Planarity : 0.003 0.029 2148 Dihedral : 8.050 56.709 2542 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.87 % Allowed : 11.76 % Favored : 86.37 % 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: -0.33 (0.22), residues: 1476 helix: 3.49 (0.27), residues: 348 sheet: 0.30 (0.36), residues: 216 loop : -2.02 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 92 HIS 0.003 0.001 HIS B 26 PHE 0.011 0.001 PHE D 9 TYR 0.010 0.001 TYR A 195 ARG 0.004 0.000 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7857 (p90) REVERT: B 27 GLN cc_start: 0.9349 (tp-100) cc_final: 0.9114 (tp-100) REVERT: B 59 MET cc_start: 0.8800 (mmm) cc_final: 0.8495 (mmm) REVERT: D 59 MET cc_start: 0.8859 (mmm) cc_final: 0.8623 (mmm) REVERT: F 2 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8828 (tm) REVERT: F 27 GLN cc_start: 0.9375 (tp-100) cc_final: 0.9056 (tp-100) REVERT: F 59 MET cc_start: 0.8761 (mmm) cc_final: 0.8493 (mmm) REVERT: E 184 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.6687 (p90) REVERT: E 239 GLN cc_start: 0.9153 (mp10) cc_final: 0.8879 (mp10) outliers start: 24 outliers final: 19 residues processed: 81 average time/residue: 0.2456 time to fit residues: 29.5415 Evaluate side-chains 78 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 97 optimal weight: 0.0000 chunk 146 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12576 Z= 0.172 Angle : 0.596 9.598 17049 Z= 0.281 Chirality : 0.043 0.245 1971 Planarity : 0.003 0.028 2148 Dihedral : 7.941 56.763 2542 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.56 % Allowed : 12.23 % Favored : 86.21 % 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: -0.24 (0.22), residues: 1476 helix: 3.53 (0.27), residues: 348 sheet: 0.37 (0.37), residues: 216 loop : -1.95 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 92 HIS 0.003 0.001 HIS F 26 PHE 0.011 0.001 PHE D 9 TYR 0.010 0.001 TYR A 195 ARG 0.005 0.000 ARG D 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.7864 (p90) REVERT: B 27 GLN cc_start: 0.9317 (tp-100) cc_final: 0.9082 (tp-100) REVERT: B 59 MET cc_start: 0.8799 (mmm) cc_final: 0.8512 (mmm) REVERT: D 59 MET cc_start: 0.8888 (mmm) cc_final: 0.8647 (mmm) REVERT: F 2 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8852 (tm) REVERT: F 27 GLN cc_start: 0.9378 (tp-100) cc_final: 0.9089 (tp-100) REVERT: F 59 MET cc_start: 0.8775 (mmm) cc_final: 0.8511 (mmm) REVERT: E 184 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.6670 (p90) REVERT: E 268 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8998 (mm) outliers start: 20 outliers final: 14 residues processed: 80 average time/residue: 0.2455 time to fit residues: 29.2316 Evaluate side-chains 73 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.043922 restraints weight = 34712.260| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 3.90 r_work: 0.2390 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 0.003 0.035 12576 Z= 0.215 Angle : 0.606 9.598 17049 Z= 0.286 Chirality : 0.044 0.242 1971 Planarity : 0.003 0.029 2148 Dihedral : 7.968 56.822 2542 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 1.64 % Allowed : 12.07 % Favored : 86.29 % 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: -0.19 (0.22), residues: 1476 helix: 3.54 (0.27), residues: 348 sheet: 0.42 (0.37), residues: 213 loop : -1.91 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 92 HIS 0.003 0.001 HIS B 26 PHE 0.012 0.001 PHE D 9 TYR 0.010 0.001 TYR A 195 ARG 0.006 0.000 ARG F 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.47 seconds wall clock time: 46 minutes 55.66 seconds (2815.66 seconds total)