Starting phenix.real_space_refine on Sat Mar 16 14:20:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqr_23950/03_2024/7mqr_23950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqr_23950/03_2024/7mqr_23950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqr_23950/03_2024/7mqr_23950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqr_23950/03_2024/7mqr_23950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqr_23950/03_2024/7mqr_23950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqr_23950/03_2024/7mqr_23950.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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 120 5.16 5 C 9416 2.51 5 N 2518 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 10": "OE1" <-> "OE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14878 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "E" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "H" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "J" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.19, per 1000 atoms: 0.55 Number of scatterers: 14878 At special positions: 0 Unit cell: (94.185, 151.515, 174.72, 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 120 16.00 O 2824 8.00 N 2518 7.00 C 9416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.04 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.02 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=1.96 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.10 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.04 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS H 7 " distance=2.09 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS H 19 " distance=2.10 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 11 " distance=2.04 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS J 7 " distance=1.97 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS J 19 " distance=1.97 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.03 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.03 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 NAG-ASN " NAG E1001 " - " ASN E 255 " " NAG E1002 " - " ASN E 25 " " NAG E1003 " - " ASN E 215 " " NAG E1004 " - " ASN E 16 " " NAG E1005 " - " ASN E 606 " " NAG E1006 " - " ASN E 624 " " NAG E1007 " - " ASN E 397 " " NAG E1008 " - " ASN E 337 " " NAG E1009 " - " ASN E 418 " " NAG E1010 " - " ASN E 111 " " NAG F1001 " - " ASN F 255 " " NAG F1002 " - " ASN F 25 " " NAG F1003 " - " ASN F 215 " " NAG F1004 " - " ASN F 16 " " NAG F1005 " - " ASN F 606 " " NAG F1006 " - " ASN F 624 " " NAG F1007 " - " ASN F 397 " " NAG F1008 " - " ASN F 337 " " NAG F1009 " - " ASN F 418 " " NAG F1010 " - " ASN F 111 " Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 3.2 seconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 30 sheets defined 18.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'B' and resid 7 through 17 removed outlier: 4.034A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 23 removed outlier: 4.338A pdb=" N ARG E 19 " --> pdb=" O ASN E 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.583A pdb=" N PHE E 46 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 4.121A pdb=" N ASP E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.520A pdb=" N ASP E 142 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 143 " --> pdb=" O VAL E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 143' Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.790A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 350 through 358 Processing helix chain 'E' and resid 435 through 447 Processing helix chain 'E' and resid 496 through 500 Processing helix chain 'E' and resid 692 through 714 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'D' and resid 7 through 17 removed outlier: 4.033A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.838A pdb=" N GLU G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'I' and resid 13 through 24 removed outlier: 3.838A pdb=" N GLU I 17 " --> pdb=" O LEU I 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 18 Processing helix chain 'F' and resid 16 through 23 removed outlier: 4.339A pdb=" N ARG F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS F 21 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 22 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.584A pdb=" N PHE F 46 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 4.121A pdb=" N ASP F 74 " --> pdb=" O SER F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 removed outlier: 3.520A pdb=" N ASP F 142 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN F 143 " --> pdb=" O VAL F 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 139 through 143' Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.790A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 350 through 358 Processing helix chain 'F' and resid 435 through 447 Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 692 through 714 Processing helix chain 'F' and resid 862 through 870 Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.592A pdb=" N LEU E 36 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 117 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL E 146 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 119 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.710A pdb=" N ILE E 57 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 82 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'E' and resid 212 through 216 removed outlier: 5.504A pdb=" N LEU E 213 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS E 228 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN E 215 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'E' and resid 252 through 254 removed outlier: 6.960A pdb=" N HIS E 247 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 321 removed outlier: 6.577A pdb=" N VAL E 335 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 313 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN E 337 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 315 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER E 339 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 317 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 341 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E 319 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LYS E 369 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 311 through 321 removed outlier: 6.577A pdb=" N VAL E 335 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 313 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN E 337 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 315 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER E 339 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 317 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 341 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E 319 " --> pdb=" O ILE E 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'E' and resid 531 through 534 removed outlier: 3.773A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL E 588 " --> pdb=" O TYR E 562 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 602 through 604 removed outlier: 3.836A pdb=" N ILE E 602 " --> pdb=" O LYS E 614 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS E 614 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 604 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 633 " --> pdb=" O ARG E 780 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 788 " --> pdb=" O ARG E 794 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 633 " --> pdb=" O ARG E 780 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E 803 " --> pdb=" O TYR E 779 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 818 through 822 Processing sheet with id=AB6, first strand: chain 'E' and resid 857 through 861 removed outlier: 4.002A pdb=" N PHE E 903 " --> pdb=" O TYR E 882 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 884 " --> pdb=" O THR E 901 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 901 " --> pdb=" O VAL E 884 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 14 removed outlier: 3.592A pdb=" N LEU F 36 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL F 117 " --> pdb=" O TYR F 144 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL F 146 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 119 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.708A pdb=" N ILE F 57 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 82 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 171 through 172 Processing sheet with id=AC1, first strand: chain 'F' and resid 212 through 216 removed outlier: 5.503A pdb=" N LEU F 213 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS F 228 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN F 215 " --> pdb=" O VAL F 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AC3, first strand: chain 'F' and resid 252 through 254 removed outlier: 6.961A pdb=" N HIS F 247 " --> pdb=" O CYS F 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.576A pdb=" N VAL F 335 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS F 313 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN F 337 " --> pdb=" O HIS F 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 315 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER F 339 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY F 317 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 341 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS F 319 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LYS F 369 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 340 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG F 371 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE F 342 " --> pdb=" O ARG F 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.576A pdb=" N VAL F 335 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS F 313 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN F 337 " --> pdb=" O HIS F 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 315 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER F 339 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY F 317 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 341 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS F 319 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 485 through 487 Processing sheet with id=AC7, first strand: chain 'F' and resid 531 through 534 removed outlier: 3.773A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE F 565 " --> pdb=" O PHE F 506 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL F 588 " --> pdb=" O TYR F 562 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 602 through 604 removed outlier: 3.836A pdb=" N ILE F 602 " --> pdb=" O LYS F 614 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 614 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 604 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL F 630 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 633 " --> pdb=" O ARG F 780 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN F 788 " --> pdb=" O ARG F 794 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL F 630 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 633 " --> pdb=" O ARG F 780 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 803 " --> pdb=" O TYR F 779 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 818 through 822 Processing sheet with id=AD3, first strand: chain 'F' and resid 857 through 861 removed outlier: 4.002A pdb=" N PHE F 903 " --> pdb=" O TYR F 882 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL F 884 " --> pdb=" O THR F 901 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 901 " --> pdb=" O VAL F 884 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 954 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: 5.24 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4812 1.35 - 1.48: 3842 1.48 - 1.61: 6422 1.61 - 1.74: 0 1.74 - 1.87: 142 Bond restraints: 15218 Sorted by residual: bond pdb=" C1 NAG F1001 " pdb=" O5 NAG F1001 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1 NAG E1001 " pdb=" O5 NAG E1001 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C1 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C1 NAG E1007 " pdb=" O5 NAG E1007 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.23e+01 ... (remaining 15213 not shown) Histogram of bond angle deviations from ideal: 97.86 - 108.63: 1080 108.63 - 119.40: 12005 119.40 - 130.17: 7407 130.17 - 140.94: 136 140.94 - 151.71: 2 Bond angle restraints: 20630 Sorted by residual: angle pdb=" CG ARG F 774 " pdb=" CD ARG F 774 " pdb=" NE ARG F 774 " ideal model delta sigma weight residual 112.00 135.38 -23.38 2.20e+00 2.07e-01 1.13e+02 angle pdb=" CG ARG E 774 " pdb=" CD ARG E 774 " pdb=" NE ARG E 774 " ideal model delta sigma weight residual 112.00 135.33 -23.33 2.20e+00 2.07e-01 1.13e+02 angle pdb=" CA LEU J 15 " pdb=" CB LEU J 15 " pdb=" CG LEU J 15 " ideal model delta sigma weight residual 116.30 151.71 -35.41 3.50e+00 8.16e-02 1.02e+02 angle pdb=" CA LEU H 15 " pdb=" CB LEU H 15 " pdb=" CG LEU H 15 " ideal model delta sigma weight residual 116.30 151.66 -35.36 3.50e+00 8.16e-02 1.02e+02 angle pdb=" CA GLU C 17 " pdb=" CB GLU C 17 " pdb=" CG GLU C 17 " ideal model delta sigma weight residual 114.10 130.19 -16.09 2.00e+00 2.50e-01 6.48e+01 ... (remaining 20625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 8671 21.73 - 43.47: 708 43.47 - 65.20: 95 65.20 - 86.93: 28 86.93 - 108.67: 16 Dihedral angle restraints: 9518 sinusoidal: 4220 harmonic: 5298 Sorted by residual: dihedral pdb=" CB CYS G 20 " pdb=" SG CYS G 20 " pdb=" SG CYS H 19 " pdb=" CB CYS H 19 " ideal model delta sinusoidal sigma weight residual -86.00 -167.48 81.48 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS I 20 " pdb=" SG CYS I 20 " pdb=" SG CYS J 19 " pdb=" CB CYS J 19 " ideal model delta sinusoidal sigma weight residual -86.00 -165.10 79.10 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA THR F 578 " pdb=" C THR F 578 " pdb=" N TYR F 579 " pdb=" CA TYR F 579 " ideal model delta harmonic sigma weight residual 180.00 136.61 43.39 0 5.00e+00 4.00e-02 7.53e+01 ... (remaining 9515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1994 0.099 - 0.198: 274 0.198 - 0.297: 42 0.297 - 0.396: 6 0.396 - 0.494: 4 Chirality restraints: 2320 Sorted by residual: chirality pdb=" CB ILE E 370 " pdb=" CA ILE E 370 " pdb=" CG1 ILE E 370 " pdb=" CG2 ILE E 370 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB VAL H 18 " pdb=" CA VAL H 18 " pdb=" CG1 VAL H 18 " pdb=" CG2 VAL H 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CB ILE F 370 " pdb=" CA ILE F 370 " pdb=" CG1 ILE F 370 " pdb=" CG2 ILE F 370 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.00e+00 ... (remaining 2317 not shown) Planarity restraints: 2652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 12 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C VAL H 12 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL H 12 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU H 13 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 12 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C VAL J 12 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL J 12 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU J 13 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 285 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO F 286 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 286 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 286 " -0.035 5.00e-02 4.00e+02 ... (remaining 2649 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5057 2.89 - 3.39: 12078 3.39 - 3.89: 25071 3.89 - 4.40: 26394 4.40 - 4.90: 44720 Nonbonded interactions: 113320 Sorted by model distance: nonbonded pdb=" O SER E 700 " pdb=" OG1 THR E 704 " model vdw 2.382 2.440 nonbonded pdb=" O SER F 700 " pdb=" OG1 THR F 704 " model vdw 2.382 2.440 nonbonded pdb=" O LYS E 310 " pdb=" OG1 THR E 334 " model vdw 2.394 2.440 nonbonded pdb=" O LYS F 310 " pdb=" OG1 THR F 334 " model vdw 2.394 2.440 nonbonded pdb=" OG1 THR E 889 " pdb=" OD1 ASN E 894 " model vdw 2.401 2.440 ... (remaining 113315 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 'G' selection = chain 'I' } ncs_group { reference = (chain 'B' and resid 5 through 20) selection = (chain 'D' and resid 5 through 20) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 4.500 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 42.060 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.007 0.102 15218 Z= 0.487 Angle : 1.323 35.411 20630 Z= 0.660 Chirality : 0.072 0.494 2320 Planarity : 0.007 0.064 2632 Dihedral : 15.731 108.669 5950 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.72 % Favored : 89.94 % Rotamer: Outliers : 0.60 % Allowed : 0.85 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.42 (0.17), residues: 1770 helix: -3.96 (0.17), residues: 256 sheet: -1.15 (0.28), residues: 328 loop : -2.34 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 832 HIS 0.008 0.001 HIS F 775 PHE 0.035 0.003 PHE E 497 TYR 0.023 0.002 TYR I 14 ARG 0.012 0.001 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: E 442 MET cc_start: 0.8940 (ttp) cc_final: 0.8648 (tmm) REVERT: E 831 MET cc_start: 0.9581 (mmp) cc_final: 0.9364 (mmp) REVERT: C 17 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: H 15 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9049 (tp) REVERT: F 556 LEU cc_start: 0.8895 (mp) cc_final: 0.8672 (mp) outliers start: 10 outliers final: 3 residues processed: 104 average time/residue: 0.2343 time to fit residues: 38.9266 Evaluate side-chains 75 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 137 optimal weight: 0.0870 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 15 GLN E 143 ASN E 295 ASN E 710 HIS C 5 GLN C 15 GLN F 143 ASN F 295 ASN F 710 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15218 Z= 0.257 Angle : 0.659 7.361 20630 Z= 0.339 Chirality : 0.047 0.208 2320 Planarity : 0.004 0.043 2632 Dihedral : 9.628 86.849 2396 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.95 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.54 (0.19), residues: 1770 helix: -2.28 (0.26), residues: 268 sheet: -0.75 (0.29), residues: 328 loop : -1.92 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 414 HIS 0.005 0.001 HIS F 32 PHE 0.018 0.002 PHE F 565 TYR 0.021 0.002 TYR E 91 ARG 0.003 0.000 ARG F 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7163 (tt0) REVERT: J 13 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7540 (tm-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2099 time to fit residues: 31.3955 Evaluate side-chains 56 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.0370 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 0.0980 chunk 158 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 143 ASN C 15 GLN F 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15218 Z= 0.138 Angle : 0.577 8.370 20630 Z= 0.294 Chirality : 0.045 0.193 2320 Planarity : 0.003 0.039 2632 Dihedral : 7.890 68.479 2396 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.61 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1770 helix: -1.58 (0.28), residues: 282 sheet: -0.34 (0.31), residues: 298 loop : -1.82 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 414 HIS 0.003 0.001 HIS F 775 PHE 0.015 0.001 PHE F 572 TYR 0.025 0.001 TYR F 579 ARG 0.009 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 ILE cc_start: 0.8466 (mm) cc_final: 0.7911 (tp) REVERT: H 12 VAL cc_start: 0.9230 (p) cc_final: 0.9015 (p) REVERT: H 13 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7238 (tt0) REVERT: J 13 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7507 (tm-30) REVERT: J 15 LEU cc_start: 0.9530 (tp) cc_final: 0.9219 (pp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2113 time to fit residues: 32.3613 Evaluate side-chains 57 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 141 optimal weight: 0.0970 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 264 HIS E 276 GLN E 328 GLN C 15 GLN F 264 HIS F 276 GLN F 328 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15218 Z= 0.194 Angle : 0.587 7.799 20630 Z= 0.298 Chirality : 0.045 0.180 2320 Planarity : 0.004 0.049 2632 Dihedral : 6.964 66.903 2396 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.06 % Favored : 92.71 % Rotamer: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.82 (0.20), residues: 1770 helix: -0.92 (0.31), residues: 284 sheet: -0.45 (0.28), residues: 338 loop : -1.59 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 414 HIS 0.004 0.001 HIS E 21 PHE 0.011 0.001 PHE E 565 TYR 0.016 0.001 TYR F 579 ARG 0.009 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 LEU cc_start: 0.9333 (mm) cc_final: 0.9021 (mm) REVERT: E 556 LEU cc_start: 0.9100 (mp) cc_final: 0.8835 (mp) REVERT: H 13 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7213 (tt0) REVERT: J 13 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7440 (tm-30) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.2183 time to fit residues: 32.0497 Evaluate side-chains 57 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 0.0050 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.0060 overall best weight: 0.9214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 34 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15218 Z= 0.157 Angle : 0.562 8.081 20630 Z= 0.284 Chirality : 0.045 0.241 2320 Planarity : 0.003 0.054 2632 Dihedral : 6.746 66.144 2396 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.61 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.56 (0.20), residues: 1770 helix: -0.44 (0.32), residues: 272 sheet: -0.52 (0.28), residues: 348 loop : -1.40 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 251 HIS 0.006 0.001 HIS F 21 PHE 0.009 0.001 PHE F 572 TYR 0.011 0.001 TYR F 849 ARG 0.006 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7864 (mm-30) REVERT: E 109 LEU cc_start: 0.9324 (mm) cc_final: 0.9061 (mm) REVERT: H 13 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7343 (tt0) REVERT: J 13 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7490 (tm-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2116 time to fit residues: 31.3483 Evaluate side-chains 59 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN C 15 GLN F 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15218 Z= 0.151 Angle : 0.560 8.433 20630 Z= 0.282 Chirality : 0.044 0.189 2320 Planarity : 0.003 0.039 2632 Dihedral : 6.569 64.884 2396 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.29 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.46 (0.20), residues: 1770 helix: -0.28 (0.32), residues: 272 sheet: -0.53 (0.28), residues: 348 loop : -1.33 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 251 HIS 0.004 0.001 HIS E 21 PHE 0.009 0.001 PHE E 565 TYR 0.012 0.001 TYR F 849 ARG 0.004 0.000 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7921 (mm-30) REVERT: H 13 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7310 (tt0) REVERT: J 13 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7470 (tm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2165 time to fit residues: 32.5508 Evaluate side-chains 63 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN C 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15218 Z= 0.172 Angle : 0.570 8.725 20630 Z= 0.286 Chirality : 0.044 0.172 2320 Planarity : 0.003 0.039 2632 Dihedral : 6.438 64.401 2396 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.51 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.37 (0.21), residues: 1770 helix: -0.15 (0.32), residues: 272 sheet: -0.48 (0.28), residues: 348 loop : -1.28 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 251 HIS 0.006 0.001 HIS E 829 PHE 0.010 0.001 PHE E 565 TYR 0.013 0.001 TYR C 14 ARG 0.003 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7995 (mm-30) REVERT: H 13 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7324 (tt0) REVERT: J 13 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7478 (tm-30) REVERT: F 806 MET cc_start: 0.8187 (ptp) cc_final: 0.7944 (mpp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2182 time to fit residues: 31.8922 Evaluate side-chains 60 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15218 Z= 0.202 Angle : 0.594 9.632 20630 Z= 0.296 Chirality : 0.046 0.410 2320 Planarity : 0.003 0.040 2632 Dihedral : 6.703 64.135 2396 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.14 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.17 (0.21), residues: 1770 helix: 0.33 (0.34), residues: 260 sheet: -0.45 (0.28), residues: 348 loop : -1.18 (0.20), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 251 HIS 0.009 0.001 HIS F 829 PHE 0.011 0.001 PHE E 565 TYR 0.011 0.001 TYR F 849 ARG 0.003 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8069 (mm-30) REVERT: H 13 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7325 (tt0) REVERT: J 13 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7434 (tm-30) REVERT: F 806 MET cc_start: 0.8142 (ptp) cc_final: 0.7914 (mpp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2134 time to fit residues: 29.0765 Evaluate side-chains 61 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 142 optimal weight: 0.0870 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15218 Z= 0.239 Angle : 0.617 10.293 20630 Z= 0.308 Chirality : 0.046 0.261 2320 Planarity : 0.003 0.040 2632 Dihedral : 6.787 63.160 2396 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.25 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1770 helix: 0.29 (0.33), residues: 260 sheet: -0.40 (0.28), residues: 338 loop : -1.20 (0.20), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 251 HIS 0.007 0.001 HIS F 829 PHE 0.017 0.001 PHE E 572 TYR 0.011 0.001 TYR F 849 ARG 0.004 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8143 (mm-30) REVERT: H 13 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7330 (tt0) REVERT: J 13 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7569 (tm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2125 time to fit residues: 27.8551 Evaluate side-chains 54 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 0.0470 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15218 Z= 0.196 Angle : 0.600 10.732 20630 Z= 0.300 Chirality : 0.046 0.278 2320 Planarity : 0.003 0.040 2632 Dihedral : 6.726 61.846 2396 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.64 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1770 helix: 0.37 (0.33), residues: 260 sheet: -0.33 (0.27), residues: 350 loop : -1.20 (0.20), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 412 HIS 0.007 0.001 HIS F 829 PHE 0.012 0.001 PHE F 381 TYR 0.049 0.001 TYR C 19 ARG 0.003 0.000 ARG F 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8149 (mm-30) REVERT: H 13 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7322 (tt0) REVERT: J 13 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7450 (tm-30) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2059 time to fit residues: 27.3568 Evaluate side-chains 56 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 143 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN C 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.089113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061111 restraints weight = 65789.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.061055 restraints weight = 40763.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060962 restraints weight = 32951.028| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15218 Z= 0.164 Angle : 0.569 10.397 20630 Z= 0.285 Chirality : 0.045 0.258 2320 Planarity : 0.003 0.039 2632 Dihedral : 6.530 61.168 2396 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.19 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.07 (0.21), residues: 1770 helix: 0.38 (0.33), residues: 260 sheet: -0.37 (0.27), residues: 362 loop : -1.12 (0.20), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 414 HIS 0.006 0.001 HIS F 829 PHE 0.017 0.001 PHE E 572 TYR 0.012 0.001 TYR F 849 ARG 0.002 0.000 ARG F 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.58 seconds wall clock time: 45 minutes 32.18 seconds (2732.18 seconds total)