Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 11:43:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/04_2023/6hjn_0234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/04_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_0234/04_2023/6hjn_0234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/04_2023/6hjn_0234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/04_2023/6hjn_0234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjn_0234/04_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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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: 8.88, per 1000 atoms: 0.72 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: 6.76 Conformation dependent library (CDL) restraints added in 2.1 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: 1.17 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: 2.92 Time building geometry restraints manager: 7.11 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 - 15.32: 6492 15.32 - 30.64: 498 30.64 - 45.96: 132 45.96 - 61.27: 15 61.27 - 76.59: 6 Dihedral angle restraints: 7143 sinusoidal: 2847 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 7140 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: 14.890 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: 0.000 Extract box with map and model: 25.920 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.020 Find NCS groups from input model: 0.820 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.170 ------------------------------------------------------------------------------- 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 : 12.086 76.592 4347 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 : 1.476 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: 0.3365 time to fit residues: 65.7769 Evaluate side-chains 64 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1072 time to fit residues: 3.1795 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7984 ------------------------------------------------------------------------------- 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: 0.8940 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12576 Z= 0.223 Angle : 0.728 9.850 17049 Z= 0.336 Chirality : 0.051 0.408 1971 Planarity : 0.004 0.031 2148 Dihedral : 5.875 59.859 1629 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.20), residues: 1476 helix: 1.79 (0.27), residues: 351 sheet: -1.36 (0.32), residues: 219 loop : -2.97 (0.16), residues: 906 *********************** 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 96 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 90 average time/residue: 0.3548 time to fit residues: 43.1371 Evaluate side-chains 66 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1297 time to fit residues: 3.8687 ------------------------------------------------------------------------------- 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: 0.0870 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 132 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 130 HIS E 184 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12576 Z= 0.176 Angle : 0.627 9.566 17049 Z= 0.298 Chirality : 0.044 0.293 1971 Planarity : 0.003 0.026 2148 Dihedral : 5.233 59.353 1629 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 1.48 % 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: -1.44 (0.21), residues: 1476 helix: 2.62 (0.27), residues: 351 sheet: -0.83 (0.33), residues: 219 loop : -2.67 (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 87 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 82 average time/residue: 0.2687 time to fit residues: 32.7162 Evaluate side-chains 54 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1163 time to fit residues: 2.5511 ------------------------------------------------------------------------------- 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: 0.6980 chunk 100 optimal weight: 0.7980 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: 0.8980 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 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 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 184 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 12576 Z= 0.340 Angle : 0.659 9.658 17049 Z= 0.319 Chirality : 0.046 0.278 1971 Planarity : 0.003 0.032 2148 Dihedral : 5.314 56.181 1629 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer Outliers : 1.48 % 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: -1.14 (0.21), residues: 1476 helix: 2.85 (0.28), residues: 351 sheet: -0.49 (0.34), residues: 216 loop : -2.51 (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 77 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 73 average time/residue: 0.2819 time to fit residues: 30.4746 Evaluate side-chains 56 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1095 time to fit residues: 3.4047 ------------------------------------------------------------------------------- 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: 0.3980 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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 196 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12576 Z= 0.199 Angle : 0.614 11.192 17049 Z= 0.294 Chirality : 0.044 0.275 1971 Planarity : 0.003 0.029 2148 Dihedral : 5.045 52.183 1629 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1476 helix: 3.10 (0.27), residues: 351 sheet: -0.31 (0.34), residues: 219 loop : -2.33 (0.18), residues: 906 *********************** 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 77 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 74 average time/residue: 0.2810 time to fit residues: 30.7629 Evaluate side-chains 61 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1162 time to fit residues: 3.7475 ------------------------------------------------------------------------------- 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: 2.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.0270 chunk 142 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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** ** 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 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: 0.8944 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12576 Z= 0.185 Angle : 0.596 9.550 17049 Z= 0.286 Chirality : 0.044 0.270 1971 Planarity : 0.003 0.029 2148 Dihedral : 4.852 47.822 1629 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % 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: -0.67 (0.22), residues: 1476 helix: 3.26 (0.27), residues: 351 sheet: -0.08 (0.35), residues: 216 loop : -2.24 (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 70 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 70 average time/residue: 0.3168 time to fit residues: 32.6139 Evaluate side-chains 52 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.619 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1234 time to fit residues: 2.3510 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 130 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** 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: 0.8940 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12576 Z= 0.179 Angle : 0.590 9.545 17049 Z= 0.283 Chirality : 0.044 0.265 1971 Planarity : 0.003 0.028 2148 Dihedral : 4.680 42.140 1629 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 0.55 % 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: -0.52 (0.22), residues: 1476 helix: 3.43 (0.27), residues: 348 sheet: 0.04 (0.36), residues: 216 loop : -2.15 (0.18), residues: 912 *********************** 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 65 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 0.2666 time to fit residues: 25.5023 Evaluate side-chains 58 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1259 time to fit residues: 2.6572 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 239 GLN ** A 250 ASN ** 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 32 HIS C 231 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN E 32 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 12576 Z= 0.433 Angle : 0.686 9.566 17049 Z= 0.335 Chirality : 0.046 0.255 1971 Planarity : 0.003 0.033 2148 Dihedral : 4.884 40.396 1629 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % 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: -0.60 (0.22), residues: 1476 helix: 3.22 (0.28), residues: 351 sheet: -0.04 (0.36), residues: 216 loop : -2.15 (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 66 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 65 average time/residue: 0.2748 time to fit residues: 26.8302 Evaluate side-chains 57 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1124 time to fit residues: 2.6685 ------------------------------------------------------------------------------- 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: 0.5980 chunk 132 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 86 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 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: 0.8954 moved from start: 0.2744 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= 0.174 Angle : 0.594 9.553 17049 Z= 0.287 Chirality : 0.044 0.262 1971 Planarity : 0.003 0.032 2148 Dihedral : 4.654 35.058 1629 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1476 helix: 3.31 (0.27), residues: 351 sheet: -0.07 (0.35), residues: 225 loop : -2.07 (0.18), residues: 900 *********************** 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 63 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 63 average time/residue: 0.2760 time to fit residues: 26.1530 Evaluate side-chains 52 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1141 time to fit residues: 2.2245 ------------------------------------------------------------------------------- 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: 3.9990 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12576 Z= 0.188 Angle : 0.602 11.455 17049 Z= 0.288 Chirality : 0.044 0.256 1971 Planarity : 0.003 0.031 2148 Dihedral : 4.510 29.930 1629 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % 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: 3.41 (0.27), residues: 351 sheet: 0.02 (0.35), residues: 225 loop : -2.00 (0.19), residues: 900 ********************** 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 58 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.2895 time to fit residues: 24.9204 Evaluate side-chains 52 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0022 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 21 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 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 = 0.2935 r_free = 0.2935 target = 0.058731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.043944 restraints weight = 34701.242| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 3.91 r_work: 0.2398 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12576 Z= 0.188 Angle : 0.600 10.415 17049 Z= 0.287 Chirality : 0.044 0.254 1971 Planarity : 0.003 0.029 2148 Dihedral : 4.471 26.552 1629 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % 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: -0.32 (0.22), residues: 1476 helix: 3.52 (0.27), residues: 348 sheet: 0.06 (0.35), residues: 225 loop : -1.97 (0.19), residues: 903 =============================================================================== Job complete usr+sys time: 2405.33 seconds wall clock time: 45 minutes 22.55 seconds (2722.55 seconds total)