Starting phenix.real_space_refine (version: dev) on Mon Feb 20 14:24:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/02_2023/6hjn_0234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/02_2023/6hjn_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_0234/02_2023/6hjn_0234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/02_2023/6hjn_0234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/02_2023/6hjn_0234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/02_2023/6hjn_0234_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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 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: 1 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: 3 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 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: 1 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: 1 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: 1 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 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: 1 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: 3 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 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 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: 1 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: 3 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 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: 18 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: 18 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: 18 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.23, per 1000 atoms: 0.59 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: 5.54 Conformation dependent library (CDL) restraints added in 1.8 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: 1.14 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: 2.97 Time building geometry restraints manager: 5.87 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=" C4 NAG L 1 " pdb=" O4 NAG L 1 " ideal model delta sigma weight residual 1.423 1.466 -0.043 1.00e-02 1.00e+04 1.81e+01 bond pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 1.423 1.464 -0.041 1.00e-02 1.00e+04 1.68e+01 ... (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=" C2 NAG L 1 " pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 109.64 101.78 7.86 5.38e-01 3.45e+00 2.13e+02 angle pdb=" C2 NAG K 1 " pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 109.64 101.90 7.74 5.38e-01 3.45e+00 2.07e+02 angle pdb=" C2 NAG M 1 " pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 109.64 101.95 7.69 5.38e-01 3.45e+00 2.04e+02 angle pdb=" C1 NAG T 1 " pdb=" C2 NAG T 1 " pdb=" C3 NAG T 1 " ideal model delta sigma weight residual 110.19 100.02 10.17 9.25e-01 1.17e+00 1.21e+02 angle pdb=" C1 NAG P 1 " pdb=" C2 NAG P 1 " pdb=" C3 NAG P 1 " ideal model delta sigma weight residual 110.19 100.02 10.17 9.25e-01 1.17e+00 1.21e+02 ... (remaining 17044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 6798 15.32 - 30.64: 513 30.64 - 45.96: 135 45.96 - 61.27: 18 61.27 - 76.59: 6 Dihedral angle restraints: 7470 sinusoidal: 3174 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 7467 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 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. 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: 9.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 34.680 Check model and map are aligned: 1.640 Process input model: 31.530 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 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 0.055 12576 Z= 0.514 Angle : 1.229 11.509 17049 Z= 0.822 Chirality : 0.111 1.434 1971 Planarity : 0.022 0.287 2148 Dihedral : 11.988 76.592 4674 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 % 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 *********************** 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 : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 6 residues processed: 147 average time/residue: 0.3390 time to fit residues: 66.0839 Evaluate side-chains 64 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1079 time to fit residues: 3.1301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 12576 Z= 0.256 Angle : 0.630 7.068 17049 Z= 0.344 Chirality : 0.045 0.230 1971 Planarity : 0.004 0.031 2148 Dihedral : 6.941 59.781 1956 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 2.26 % 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: -2.17 (0.20), residues: 1476 helix: 1.74 (0.28), residues: 351 sheet: -1.32 (0.32), residues: 213 loop : -2.99 (0.16), residues: 912 *********************** 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 97 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 9 residues processed: 91 average time/residue: 0.3452 time to fit residues: 42.4952 Evaluate side-chains 66 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1105 time to fit residues: 3.5540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** 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 E 184 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 12576 Z= 0.291 Angle : 0.587 8.252 17049 Z= 0.322 Chirality : 0.044 0.288 1971 Planarity : 0.003 0.027 2148 Dihedral : 6.441 59.810 1956 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer Outliers : 1.56 % 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: -1.51 (0.21), residues: 1476 helix: 2.54 (0.28), residues: 351 sheet: -0.85 (0.33), residues: 219 loop : -2.71 (0.17), residues: 906 *********************** 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 84 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 78 average time/residue: 0.2697 time to fit residues: 31.2929 Evaluate side-chains 55 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1122 time to fit residues: 2.4472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 25 HIS ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 12576 Z= 0.417 Angle : 0.635 10.454 17049 Z= 0.343 Chirality : 0.045 0.246 1971 Planarity : 0.003 0.034 2148 Dihedral : 6.464 55.906 1956 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 1.95 % 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 (0.21), residues: 1476 helix: 2.78 (0.28), residues: 351 sheet: -0.47 (0.35), residues: 216 loop : -2.53 (0.17), residues: 909 *********************** 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 84 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 59 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 81 average time/residue: 0.2789 time to fit residues: 33.0326 Evaluate side-chains 61 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1113 time to fit residues: 4.2210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 121 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 130 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS E 130 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: 0.9118 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 12576 Z= 0.246 Angle : 0.572 7.623 17049 Z= 0.310 Chirality : 0.044 0.252 1971 Planarity : 0.003 0.031 2148 Dihedral : 6.190 51.895 1956 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1476 helix: 3.07 (0.27), residues: 351 sheet: -0.19 (0.35), residues: 216 loop : -2.37 (0.18), residues: 909 *********************** 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 76 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 72 average time/residue: 0.3084 time to fit residues: 31.8733 Evaluate side-chains 57 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1180 time to fit residues: 2.4391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 142 optimal weight: 0.0970 chunk 118 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** 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** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 12576 Z= 0.293 Angle : 0.573 7.080 17049 Z= 0.312 Chirality : 0.044 0.239 1971 Planarity : 0.003 0.033 2148 Dihedral : 6.075 49.811 1956 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 0.86 % 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: -0.74 (0.22), residues: 1476 helix: 3.17 (0.27), residues: 351 sheet: -0.08 (0.36), residues: 216 loop : -2.29 (0.18), residues: 909 *********************** 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 69 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 67 average time/residue: 0.2981 time to fit residues: 29.1593 Evaluate side-chains 57 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1075 time to fit residues: 2.1915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 0.0010 chunk 79 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 12576 Z= 0.202 Angle : 0.544 8.413 17049 Z= 0.297 Chirality : 0.043 0.234 1971 Planarity : 0.003 0.029 2148 Dihedral : 5.930 49.229 1956 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 0.86 % 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: -0.59 (0.22), residues: 1476 helix: 3.26 (0.27), residues: 351 sheet: 0.12 (0.36), residues: 216 loop : -2.20 (0.18), residues: 909 *********************** 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 68 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 0 residues processed: 67 average time/residue: 0.3078 time to fit residues: 30.1380 Evaluate side-chains 52 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 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 32 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 12576 Z= 0.360 Angle : 0.609 9.702 17049 Z= 0.327 Chirality : 0.044 0.231 1971 Planarity : 0.003 0.033 2148 Dihedral : 6.037 45.814 1956 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1476 helix: 3.25 (0.27), residues: 351 sheet: 0.09 (0.36), residues: 216 loop : -2.14 (0.18), residues: 909 *********************** 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 63 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.2720 time to fit residues: 25.4929 Evaluate side-chains 55 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1248 time to fit residues: 3.0037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 296 GLN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 12576 Z= 0.257 Angle : 0.568 9.871 17049 Z= 0.308 Chirality : 0.043 0.226 1971 Planarity : 0.003 0.032 2148 Dihedral : 5.905 44.506 1956 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 0.23 % 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: -0.46 (0.22), residues: 1476 helix: 3.28 (0.27), residues: 351 sheet: 0.21 (0.36), residues: 216 loop : -2.08 (0.18), residues: 909 *********************** 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 56 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.2739 time to fit residues: 22.8659 Evaluate side-chains 52 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1271 time to fit residues: 2.1346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 66 optimal weight: 0.0040 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 116 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0.9088 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 12576 Z= 0.205 Angle : 0.551 10.232 17049 Z= 0.299 Chirality : 0.042 0.218 1971 Planarity : 0.003 0.029 2148 Dihedral : 5.719 44.120 1956 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 0.08 % 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: -0.38 (0.22), residues: 1476 helix: 3.42 (0.27), residues: 348 sheet: 0.09 (0.36), residues: 225 loop : -2.02 (0.19), residues: 903 ********************** 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 59 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.3066 time to fit residues: 26.9580 Evaluate side-chains 52 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 102 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** 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 = 0.2937 r_free = 0.2937 target = 0.058808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.044069 restraints weight = 34765.194| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 3.90 r_work: 0.2395 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 12576 Z= 0.228 Angle : 0.556 9.716 17049 Z= 0.300 Chirality : 0.043 0.216 1971 Planarity : 0.003 0.031 2148 Dihedral : 5.625 44.850 1956 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 0.23 % 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: -0.31 (0.22), residues: 1476 helix: 3.49 (0.27), residues: 348 sheet: 0.12 (0.36), residues: 225 loop : -1.96 (0.19), residues: 903 =============================================================================== Job complete usr+sys time: 2416.53 seconds wall clock time: 46 minutes 6.27 seconds (2766.27 seconds total)