Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 12:34:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/10_2023/8kd4_37124_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/10_2023/8kd4_37124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/10_2023/8kd4_37124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/10_2023/8kd4_37124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/10_2023/8kd4_37124_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd4_37124/10_2023/8kd4_37124_updated.pdb" } resolution = 2.93 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= 0.002 sd= 0.011 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 328 5.49 5 S 91 5.16 5 C 16152 2.51 5 N 4810 2.21 5 O 5682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 376": "OD1" <-> "OD2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 308": "OE1" <-> "OE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 133": "OE1" <-> "OE2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 48": "OD1" <-> "OD2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "S ASP 106": "OD1" <-> "OD2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "U ASP 90": "OD1" <-> "OD2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "V TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "V GLU 90": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 811": "OE1" <-> "OE2" Residue "B GLU 813": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 951": "OE1" <-> "OE2" Residue "B ASP 958": "OD1" <-> "OD2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1012": "OD1" <-> "OD2" Residue "B PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1027": "OE1" <-> "OE2" Residue "B PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1166": "OE1" <-> "OE2" Residue "B ASP 1183": "OD1" <-> "OD2" Residue "B GLU 1193": "OE1" <-> "OE2" Residue "B GLU 1264": "OE1" <-> "OE2" Residue "B PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1306": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E ASP 377": "OD1" <-> "OD2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "E GLU 544": "OE1" <-> "OE2" Residue "G GLU 323": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 27064 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1883 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 2 Chain: "F" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1639 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 2 Chain: "O" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4545 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 12, 'TRANS': 529} Chain breaks: 2 Chain: "E" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2611 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain breaks: 3 Chain: "G" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.59, per 1000 atoms: 0.50 Number of scatterers: 27064 At special positions: 0 Unit cell: (138.45, 161.88, 186.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 91 16.00 P 328 15.00 O 5682 8.00 N 4810 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " 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 Time building additional restraints: 11.84 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 4 sheets defined 51.0% alpha, 2.2% beta 140 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 11.63 Creating SS restraints... Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 226 through 240 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 274 through 294 removed outlier: 5.483A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 316 removed outlier: 4.625A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 328 through 343 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 368 Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 230 through 238 removed outlier: 3.989A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 removed outlier: 4.075A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 289 removed outlier: 4.500A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 329 through 344 removed outlier: 4.301A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Proline residue: F 339 - end of helix removed outlier: 3.735A pdb=" N SER F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 367 Processing helix chain 'O' and resid 45 through 54 Processing helix chain 'O' and resid 64 through 77 removed outlier: 3.544A pdb=" N LEU O 70 " --> pdb=" O PRO O 66 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 113 Processing helix chain 'O' and resid 121 through 131 Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 31 through 40 Processing helix chain 'P' and resid 50 through 75 removed outlier: 4.025A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 93 removed outlier: 4.005A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 20 No H-bonds generated for 'chain 'Q' and resid 17 through 20' Processing helix chain 'Q' and resid 27 through 36 Processing helix chain 'Q' and resid 45 through 72 removed outlier: 4.344A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'R' and resid 35 through 45 removed outlier: 3.687A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 80 Processing helix chain 'R' and resid 88 through 98 Processing helix chain 'R' and resid 101 through 119 removed outlier: 3.924A pdb=" N HIS R 106 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL R 108 " --> pdb=" O LYS R 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR R 112 " --> pdb=" O SER R 109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS R 113 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR R 116 " --> pdb=" O LYS R 113 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR R 119 " --> pdb=" O THR R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 55 Processing helix chain 'S' and resid 64 through 78 removed outlier: 3.619A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 113 Processing helix chain 'S' and resid 121 through 131 Processing helix chain 'T' and resid 26 through 28 No H-bonds generated for 'chain 'T' and resid 26 through 28' Processing helix chain 'T' and resid 31 through 40 Processing helix chain 'T' and resid 50 through 75 removed outlier: 3.824A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 93 removed outlier: 4.137A pdb=" N GLN T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 20 No H-bonds generated for 'chain 'U' and resid 17 through 20' Processing helix chain 'U' and resid 27 through 36 Processing helix chain 'U' and resid 45 through 72 removed outlier: 4.039A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 91 through 96 Processing helix chain 'V' and resid 35 through 45 Processing helix chain 'V' and resid 53 through 80 Processing helix chain 'V' and resid 88 through 98 Processing helix chain 'V' and resid 101 through 118 removed outlier: 3.615A pdb=" N HIS V 106 " --> pdb=" O LEU V 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR V 116 " --> pdb=" O LYS V 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 57 through 60 removed outlier: 3.554A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 244 through 261 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 288 through 299 removed outlier: 3.866A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.751A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 366 through 382 removed outlier: 4.969A pdb=" N ASN A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 665 through 676 removed outlier: 4.601A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 699 through 709 removed outlier: 3.711A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 802 through 839 removed outlier: 3.604A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'B' and resid 873 through 885 removed outlier: 3.884A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 928 removed outlier: 3.923A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 942 removed outlier: 4.290A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.606A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 996 Processing helix chain 'B' and resid 1004 through 1021 removed outlier: 4.059A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1163 Processing helix chain 'B' and resid 1165 through 1173 removed outlier: 3.877A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1184 Processing helix chain 'B' and resid 1203 through 1215 Processing helix chain 'B' and resid 1221 through 1229 Processing helix chain 'B' and resid 1237 through 1239 No H-bonds generated for 'chain 'B' and resid 1237 through 1239' Processing helix chain 'B' and resid 1242 through 1258 removed outlier: 3.596A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1272 Processing helix chain 'B' and resid 1283 through 1293 Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 304 through 307 No H-bonds generated for 'chain 'E' and resid 304 through 307' Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.734A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 344 removed outlier: 4.479A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 431 through 433 No H-bonds generated for 'chain 'E' and resid 431 through 433' Processing helix chain 'E' and resid 544 through 560 removed outlier: 4.599A pdb=" N MET E 560 " --> pdb=" O TYR E 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 325 No H-bonds generated for 'chain 'G' and resid 323 through 325' Processing helix chain 'G' and resid 338 through 343 removed outlier: 4.171A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 343' Processing helix chain 'G' and resid 542 through 568 Processing sheet with id= A, first strand: chain 'D' and resid 244 through 246 Processing sheet with id= B, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.932A pdb=" N GLU A 62 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 23 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 141 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE A 24 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 143 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET A 305 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN A 144 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 307 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id= D, first strand: chain 'E' and resid 272 through 274 840 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 13.79 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6715 1.34 - 1.46: 7613 1.46 - 1.58: 13159 1.58 - 1.70: 654 1.70 - 1.82: 144 Bond restraints: 28285 Sorted by residual: bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.708 -0.216 5.00e-02 4.00e+02 1.86e+01 bond pdb=" CA SER A 408 " pdb=" C SER A 408 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.40e-02 5.10e+03 1.32e+01 bond pdb=" CG PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.503 1.402 0.101 3.40e-02 8.65e+02 8.76e+00 bond pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.00e+00 bond pdb=" C ASN B1004 " pdb=" N PRO B1005 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 7.94e+00 ... (remaining 28280 not shown) Histogram of bond angle deviations from ideal: 93.25 - 102.11: 354 102.11 - 110.98: 11619 110.98 - 119.84: 14733 119.84 - 128.71: 12500 128.71 - 137.57: 373 Bond angle restraints: 39579 Sorted by residual: angle pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 112.00 96.38 15.62 1.40e+00 5.10e-01 1.24e+02 angle pdb=" N PRO D 319 " pdb=" CD PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 103.20 93.25 9.95 1.50e+00 4.44e-01 4.40e+01 angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.58 -11.48 2.00e+00 2.50e-01 3.29e+01 angle pdb=" CA GLU E 507 " pdb=" CB GLU E 507 " pdb=" CG GLU E 507 " ideal model delta sigma weight residual 114.10 124.92 -10.82 2.00e+00 2.50e-01 2.93e+01 angle pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " pdb=" CG LEU F 297 " ideal model delta sigma weight residual 116.30 133.36 -17.06 3.50e+00 8.16e-02 2.38e+01 ... (remaining 39574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13841 35.18 - 70.36: 2007 70.36 - 105.54: 47 105.54 - 140.72: 2 140.72 - 175.89: 1 Dihedral angle restraints: 15898 sinusoidal: 8559 harmonic: 7339 Sorted by residual: dihedral pdb=" CA LEU B1184 " pdb=" C LEU B1184 " pdb=" N ASP B1185 " pdb=" CA ASP B1185 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLU B1220 " pdb=" C GLU B1220 " pdb=" N HIS B1221 " pdb=" CA HIS B1221 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET D 347 " pdb=" C MET D 347 " pdb=" N ASP D 348 " pdb=" CA ASP D 348 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 15895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4131 0.086 - 0.173: 228 0.173 - 0.259: 6 0.259 - 0.345: 4 0.345 - 0.432: 1 Chirality restraints: 4370 Sorted by residual: chirality pdb=" CG LEU B 825 " pdb=" CB LEU B 825 " pdb=" CD1 LEU B 825 " pdb=" CD2 LEU B 825 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" C PRO D 319 " pdb=" CB PRO D 319 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL F 364 " pdb=" CA VAL F 364 " pdb=" CG1 VAL F 364 " pdb=" CG2 VAL F 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4367 not shown) Planarity restraints: 3885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 318 " 0.059 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO D 319 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.018 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 775 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 492 " 0.015 2.00e-02 2.50e+03 1.76e-02 7.75e+00 pdb=" CG TRP E 492 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP E 492 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 492 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 492 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 492 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 492 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 492 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 492 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 492 " -0.001 2.00e-02 2.50e+03 ... (remaining 3882 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 240 2.60 - 3.17: 21452 3.17 - 3.75: 48655 3.75 - 4.32: 63258 4.32 - 4.90: 95653 Nonbonded interactions: 229258 Sorted by model distance: nonbonded pdb=" CD2 LEU B 883 " pdb=" OG1 THR B 890 " model vdw 2.023 3.460 nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.036 2.104 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.122 3.880 nonbonded pdb=" OG SER A 123 " pdb=" OD2 ASP A 165 " model vdw 2.222 2.440 nonbonded pdb=" OG SER D 392 " pdb=" OE1 GLU A 156 " model vdw 2.227 2.440 ... (remaining 229253 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 'D' and (resid 11 through 24 or resid 80 through 112 or resid 222 through \ 373)) selection = chain 'F' } ncs_group { reference = (chain 'O' and resid 37 through 133) selection = (chain 'S' and resid 37 through 133) } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } 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: 8.320 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: 33.820 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 86.320 Find NCS groups from input model: 0.870 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: 0.010 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.004 0.216 28285 Z= 0.256 Angle : 0.809 17.062 39579 Z= 0.429 Chirality : 0.042 0.432 4370 Planarity : 0.005 0.095 3885 Dihedral : 24.502 175.895 11153 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 0.59 % Allowed : 32.67 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 2447 helix: -0.45 (0.13), residues: 1312 sheet: 0.18 (0.64), residues: 85 loop : -1.70 (0.17), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 354 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 361 average time/residue: 1.2677 time to fit residues: 542.3052 Evaluate side-chains 312 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 304 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.3041 time to fit residues: 5.2262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 267 GLN F 350 GLN P 27 GLN S 85 GLN U 38 ASN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 419 GLN B1150 HIS E 314 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 28285 Z= 0.351 Angle : 0.679 12.314 39579 Z= 0.368 Chirality : 0.042 0.209 4370 Planarity : 0.005 0.060 3885 Dihedral : 27.032 178.976 6038 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 6.08 % Allowed : 26.36 % Favored : 67.55 % 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: -0.94 (0.16), residues: 2447 helix: -0.02 (0.14), residues: 1353 sheet: 0.40 (0.59), residues: 91 loop : -1.49 (0.18), residues: 1003 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 365 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 35 residues processed: 452 average time/residue: 1.4802 time to fit residues: 773.7845 Evaluate side-chains 324 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 10 average time/residue: 0.5238 time to fit residues: 11.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN F 263 HIS O 68 GLN O 76 GLN O 108 ASN R 46 HIS R 106 HIS S 76 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 125 GLN ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS B1254 HIS E 314 ASN E 410 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28285 Z= 0.244 Angle : 0.586 11.640 39579 Z= 0.319 Chirality : 0.038 0.183 4370 Planarity : 0.004 0.047 3885 Dihedral : 27.051 177.562 6038 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.45 % Allowed : 26.36 % Favored : 68.18 % 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: -0.52 (0.16), residues: 2447 helix: 0.37 (0.14), residues: 1346 sheet: 0.11 (0.56), residues: 91 loop : -1.31 (0.19), residues: 1010 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 335 time to evaluate : 2.486 Fit side-chains revert: symmetry clash outliers start: 121 outliers final: 47 residues processed: 418 average time/residue: 1.4439 time to fit residues: 702.7643 Evaluate side-chains 349 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 302 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 32 residues processed: 16 average time/residue: 0.7049 time to fit residues: 18.4249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 249 optimal weight: 0.2980 chunk 263 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN R 46 HIS S 76 GLN S 108 ASN V 46 HIS ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B1150 HIS B1221 HIS E 314 ASN E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28285 Z= 0.272 Angle : 0.599 10.799 39579 Z= 0.325 Chirality : 0.038 0.251 4370 Planarity : 0.004 0.039 3885 Dihedral : 27.099 178.263 6038 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.27 % Allowed : 27.22 % Favored : 67.51 % 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: -0.37 (0.17), residues: 2447 helix: 0.51 (0.14), residues: 1343 sheet: -0.24 (0.55), residues: 90 loop : -1.21 (0.19), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 340 time to evaluate : 2.717 Fit side-chains revert: symmetry clash outliers start: 117 outliers final: 53 residues processed: 419 average time/residue: 1.3934 time to fit residues: 680.6511 Evaluate side-chains 353 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 300 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 35 residues processed: 19 average time/residue: 0.5375 time to fit residues: 17.7864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN O 39 HIS R 46 HIS S 76 GLN T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 HIS B1222 GLN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28285 Z= 0.340 Angle : 0.636 11.496 39579 Z= 0.347 Chirality : 0.040 0.251 4370 Planarity : 0.004 0.063 3885 Dihedral : 27.313 178.473 6038 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 5.81 % Allowed : 26.72 % Favored : 67.46 % 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: -0.48 (0.17), residues: 2447 helix: 0.40 (0.14), residues: 1350 sheet: -0.67 (0.53), residues: 90 loop : -1.21 (0.19), residues: 1007 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 326 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 51 residues processed: 418 average time/residue: 1.4608 time to fit residues: 708.5347 Evaluate side-chains 347 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 296 time to evaluate : 2.732 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 37 residues processed: 14 average time/residue: 0.5956 time to fit residues: 14.8899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.9990 chunk 237 optimal weight: 0.0870 chunk 52 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 GLN E 314 ASN E 410 ASN E 459 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28285 Z= 0.208 Angle : 0.598 12.538 39579 Z= 0.322 Chirality : 0.038 0.369 4370 Planarity : 0.004 0.039 3885 Dihedral : 27.210 176.530 6038 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.64 % Allowed : 28.44 % Favored : 66.92 % 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: -0.27 (0.17), residues: 2447 helix: 0.61 (0.14), residues: 1345 sheet: -0.76 (0.53), residues: 90 loop : -1.15 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 340 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 55 residues processed: 414 average time/residue: 1.4505 time to fit residues: 695.4798 Evaluate side-chains 355 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 2.465 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 43 residues processed: 12 average time/residue: 0.3319 time to fit residues: 9.7743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 160 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN O 76 GLN P 93 GLN R 46 HIS T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN B1222 GLN E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28285 Z= 0.275 Angle : 0.632 13.395 39579 Z= 0.338 Chirality : 0.039 0.330 4370 Planarity : 0.004 0.046 3885 Dihedral : 27.251 177.729 6038 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.83 % Allowed : 29.61 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2447 helix: 0.54 (0.14), residues: 1363 sheet: -0.80 (0.53), residues: 90 loop : -1.12 (0.19), residues: 994 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 319 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 50 residues processed: 384 average time/residue: 1.5049 time to fit residues: 672.2319 Evaluate side-chains 351 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 301 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 41 residues processed: 9 average time/residue: 0.5713 time to fit residues: 10.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 79 optimal weight: 0.0020 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 167 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 206 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN R 46 HIS ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28285 Z= 0.197 Angle : 0.613 13.859 39579 Z= 0.328 Chirality : 0.038 0.322 4370 Planarity : 0.004 0.047 3885 Dihedral : 27.176 175.547 6038 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.61 % Allowed : 29.70 % Favored : 66.70 % 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: -0.21 (0.17), residues: 2447 helix: 0.62 (0.14), residues: 1356 sheet: -0.73 (0.54), residues: 90 loop : -1.07 (0.19), residues: 1001 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 310 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 45 residues processed: 373 average time/residue: 1.4237 time to fit residues: 618.8021 Evaluate side-chains 334 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 289 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 41 residues processed: 4 average time/residue: 0.2946 time to fit residues: 5.3752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 20.0000 chunk 252 optimal weight: 30.0000 chunk 229 optimal weight: 0.4980 chunk 245 optimal weight: 0.0370 chunk 147 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 221 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 HIS ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28285 Z= 0.206 Angle : 0.631 16.093 39579 Z= 0.333 Chirality : 0.038 0.344 4370 Planarity : 0.004 0.047 3885 Dihedral : 27.100 176.558 6038 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.15 % Allowed : 30.15 % Favored : 66.70 % 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: -0.17 (0.17), residues: 2447 helix: 0.66 (0.14), residues: 1355 sheet: -0.69 (0.54), residues: 90 loop : -1.08 (0.19), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 300 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 45 residues processed: 356 average time/residue: 1.5068 time to fit residues: 623.1536 Evaluate side-chains 333 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 288 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 40 residues processed: 5 average time/residue: 0.5179 time to fit residues: 7.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 3.9990 chunk 259 optimal weight: 0.4980 chunk 158 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 180 optimal weight: 0.0030 chunk 271 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 216 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.7092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 HIS T 25 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28285 Z= 0.220 Angle : 0.635 14.679 39579 Z= 0.335 Chirality : 0.038 0.347 4370 Planarity : 0.004 0.053 3885 Dihedral : 27.083 175.864 6038 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.79 % Allowed : 30.73 % Favored : 66.47 % 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: -0.20 (0.17), residues: 2447 helix: 0.63 (0.14), residues: 1354 sheet: -0.64 (0.55), residues: 90 loop : -1.08 (0.19), residues: 1003 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4894 Ramachandran restraints generated. 2447 Oldfield, 0 Emsley, 2447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 306 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 44 residues processed: 357 average time/residue: 1.4487 time to fit residues: 601.8808 Evaluate side-chains 333 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 2.761 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 38 residues processed: 6 average time/residue: 0.7769 time to fit residues: 9.4781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.0970 chunk 230 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 199 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 216 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 222 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN Q 104 GLN R 46 HIS ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 GLN E 410 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088480 restraints weight = 56489.432| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.93 r_work: 0.3208 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28285 Z= 0.214 Angle : 0.647 18.740 39579 Z= 0.338 Chirality : 0.038 0.351 4370 Planarity : 0.004 0.056 3885 Dihedral : 27.052 175.628 6038 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.43 % Allowed : 31.10 % Favored : 66.47 % 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: -0.16 (0.17), residues: 2447 helix: 0.65 (0.14), residues: 1352 sheet: -0.65 (0.55), residues: 90 loop : -1.04 (0.19), residues: 1005 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10996.68 seconds wall clock time: 196 minutes 31.13 seconds (11791.13 seconds total)