Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 10:10:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/10_2023/8kd5_37125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/10_2023/8kd5_37125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/10_2023/8kd5_37125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/10_2023/8kd5_37125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/10_2023/8kd5_37125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd5_37125/10_2023/8kd5_37125_updated.pdb" } resolution = 2.9 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 319 5.49 5 S 91 5.16 5 C 16088 2.51 5 N 4778 2.21 5 O 5631 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 TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F GLU 255": "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 360": "OE1" <-> "OE2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O ASP 106": "OD1" <-> "OD2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "R TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 106": "OD1" <-> "OD2" Residue "S ASP 123": "OD1" <-> "OD2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T ASP 85": "OD1" <-> "OD2" Residue "U ASP 90": "OD1" <-> "OD2" Residue "V TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 65": "OD1" <-> "OD2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "V GLU 90": "OE1" <-> "OE2" Residue "V GLU 102": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 780": "OD1" <-> "OD2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1012": "OD1" <-> "OD2" Residue "B TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1225": "OE1" <-> "OE2" Residue "B TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1259": "OD1" <-> "OD2" Residue "B ASP 1282": "OD1" <-> "OD2" Residue "B ASP 1320": "OD1" <-> "OD2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 344": "OD1" <-> "OD2" Residue "E TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 550": "OD1" <-> "OD2" Residue "G PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 26908 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 2 Chain: "F" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1573 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 2 Chain: "O" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: "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: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3277 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "Y" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3261 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} 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: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4519 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 12, 'TRANS': 526} 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: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 724 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} 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: 13.56, per 1000 atoms: 0.50 Number of scatterers: 26908 At special positions: 0 Unit cell: (139.87, 152.65, 188.15, 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 319 15.00 O 5631 8.00 N 4778 7.00 C 16088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 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: 12.19 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 3 sheets defined 51.6% alpha, 2.4% beta 133 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 11.93 Creating SS restraints... Processing helix chain 'D' and resid 99 through 111 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 292 Processing helix chain 'D' and resid 300 through 315 removed outlier: 4.505A pdb=" N LEU D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (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 342 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 368 Processing helix chain 'D' and resid 392 through 399 Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 230 through 236 Processing helix chain 'F' and resid 254 through 264 removed outlier: 4.054A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 289 removed outlier: 4.374A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 329 through 342 removed outlier: 3.537A pdb=" N LEU F 332 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU F 338 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Proline residue: F 339 - end of helix Processing helix chain 'F' and resid 349 through 368 removed outlier: 4.517A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 56 removed outlier: 3.581A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 77 removed outlier: 3.970A 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: 4.020A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 93 removed outlier: 4.020A 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: 3.622A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 80 removed outlier: 3.538A pdb=" N TYR R 80 " --> pdb=" O ARG R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 98 Processing helix chain 'R' and resid 101 through 119 removed outlier: 3.712A pdb=" N LYS R 105 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS R 106 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR R 112 " --> pdb=" O SER R 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS R 113 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 116 " --> pdb=" O LYS R 113 " (cutoff:3.500A) removed outlier: 3.649A 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: 3.640A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.826A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 91 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: 4.036A 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: 3.750A pdb=" N LYS V 105 " --> pdb=" O GLU V 102 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL V 108 " --> pdb=" O LYS V 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU V 110 " --> pdb=" O ALA V 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.588A pdb=" N ILE A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 99 through 103 removed outlier: 4.104A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' 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 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 288 through 301 removed outlier: 4.007A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 301 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.723A 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: 4.905A 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: 4.459A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 4.928A 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: 3.628A 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: 3.788A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.669A 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: 3.749A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 928 removed outlier: 4.026A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 942 removed outlier: 4.194A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.744A 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: 3.787A 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: 4.121A 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 1216 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: 3.585A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.529A 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 56 removed outlier: 4.031A pdb=" N SER E 56 " --> pdb=" O ILE E 53 " (cutoff:3.500A) 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 309 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 334 through 344 removed outlier: 4.146A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' 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: 5.112A pdb=" N MET E 560 " --> pdb=" O TYR E 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 311 Processing helix chain 'G' and resid 322 through 328 removed outlier: 3.699A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS G 328 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 removed outlier: 3.975A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) removed outlier: 4.122A 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 'A' and resid 62 through 64 removed outlier: 3.717A pdb=" N GLU A 62 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 141 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE A 24 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 143 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET A 305 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASN A 144 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 307 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 310 " --> pdb=" O CYS A 271 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id= C, first strand: chain 'E' and resid 272 through 275 removed outlier: 4.115A pdb=" N CYS E 275 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS E 280 " --> pdb=" O CYS E 275 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 15.76 Time building geometry restraints manager: 12.96 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: 7634 1.34 - 1.47: 8286 1.47 - 1.59: 11407 1.59 - 1.72: 636 1.72 - 1.85: 142 Bond restraints: 28105 Sorted by residual: bond pdb=" C MET B 765 " pdb=" N PRO B 766 " ideal model delta sigma weight residual 1.334 1.377 -0.043 1.51e-02 4.39e+03 8.05e+00 bond pdb=" N VAL A 102 " pdb=" CA VAL A 102 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" C ASN B1004 " pdb=" N PRO B1005 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.36e-02 5.41e+03 6.82e+00 bond pdb=" N LYS A 103 " pdb=" CA LYS A 103 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.70e+00 bond pdb=" N ASN E 347 " pdb=" CA ASN E 347 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.45e-02 4.76e+03 5.50e+00 ... (remaining 28100 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.39: 1630 105.39 - 112.56: 14718 112.56 - 119.73: 9709 119.73 - 126.90: 12244 126.90 - 134.07: 995 Bond angle restraints: 39296 Sorted by residual: angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.61 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" CB LYS B 962 " pdb=" CG LYS B 962 " pdb=" CD LYS B 962 " ideal model delta sigma weight residual 111.30 122.72 -11.42 2.30e+00 1.89e-01 2.47e+01 angle pdb=" CB MET S 90 " pdb=" CG MET S 90 " pdb=" SD MET S 90 " ideal model delta sigma weight residual 112.70 127.53 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA GLN F 305 " pdb=" CB GLN F 305 " pdb=" CG GLN F 305 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CB MET O 90 " pdb=" CG MET O 90 " pdb=" SD MET O 90 " ideal model delta sigma weight residual 112.70 126.23 -13.53 3.00e+00 1.11e-01 2.03e+01 ... (remaining 39291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13820 35.18 - 70.36: 1956 70.36 - 105.55: 51 105.55 - 140.73: 2 140.73 - 175.91: 1 Dihedral angle restraints: 15830 sinusoidal: 8478 harmonic: 7352 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 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA MET F 347 " pdb=" C MET F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA HIS E 302 " pdb=" C HIS E 302 " pdb=" N CYS E 303 " pdb=" CA CYS E 303 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 15827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3613 0.052 - 0.103: 606 0.103 - 0.155: 111 0.155 - 0.207: 11 0.207 - 0.259: 2 Chirality restraints: 4343 Sorted by residual: chirality pdb=" CB ILE F 105 " pdb=" CA ILE F 105 " pdb=" CG1 ILE F 105 " pdb=" CG2 ILE F 105 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL B 777 " pdb=" CA VAL B 777 " pdb=" CG1 VAL B 777 " pdb=" CG2 VAL B 777 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU F 338 " pdb=" CB LEU F 338 " pdb=" CD1 LEU F 338 " pdb=" CD2 LEU F 338 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4340 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 321 " -0.088 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO D 322 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 292 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO E 293 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 293 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 293 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 775 " 0.015 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP B 775 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 775 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 775 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 775 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 775 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 775 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 775 " -0.002 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 345 2.62 - 3.19: 21779 3.19 - 3.76: 48297 3.76 - 4.33: 62563 4.33 - 4.90: 94768 Nonbonded interactions: 227752 Sorted by model distance: nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.044 2.104 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.139 3.880 nonbonded pdb=" O ASN B1165 " pdb=" OG1 THR B1169 " model vdw 2.221 2.440 nonbonded pdb=" O LYS D 243 " pdb=" OG1 THR D 390 " model vdw 2.234 2.440 nonbonded pdb=" O ILE E 395 " pdb=" NZ LYS E 397 " model vdw 2.260 2.520 ... (remaining 227747 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 'O' and resid 36 through 133) selection = chain 'S' } 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=0.00 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: 10.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 33.620 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 87.460 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.003 0.058 28105 Z= 0.211 Angle : 0.749 14.828 39296 Z= 0.400 Chirality : 0.040 0.259 4343 Planarity : 0.005 0.131 3879 Dihedral : 24.439 175.912 11073 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.29 % Favored : 95.59 % Rotamer: Outliers : 0.54 % Allowed : 32.75 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 2450 helix: -0.12 (0.13), residues: 1323 sheet: 0.76 (0.67), residues: 81 loop : -1.75 (0.17), residues: 1046 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 315 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 319 average time/residue: 1.2223 time to fit residues: 462.2068 Evaluate side-chains 289 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 286 time to evaluate : 2.521 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.3902 time to fit residues: 3.8877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 267 GLN F 305 GLN O 39 HIS O 108 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 GLN U 38 ASN V 60 ASN A 31 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1190 GLN ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 HIS ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 28105 Z= 0.394 Angle : 0.687 12.640 39296 Z= 0.374 Chirality : 0.042 0.221 4343 Planarity : 0.005 0.084 3879 Dihedral : 27.073 178.992 5952 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.80 % Allowed : 25.91 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2450 helix: 0.24 (0.14), residues: 1352 sheet: 0.08 (0.58), residues: 92 loop : -1.42 (0.18), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 350 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 38 residues processed: 437 average time/residue: 1.4413 time to fit residues: 731.3178 Evaluate side-chains 326 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 288 time to evaluate : 2.555 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 11 average time/residue: 0.4245 time to fit residues: 10.4940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 247 optimal weight: 0.8980 chunk 267 optimal weight: 0.0070 chunk 220 optimal weight: 0.6980 chunk 245 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS Q 38 ASN V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1143 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28105 Z= 0.190 Angle : 0.559 11.379 39296 Z= 0.305 Chirality : 0.036 0.252 4343 Planarity : 0.004 0.069 3879 Dihedral : 27.066 176.001 5952 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.90 % Allowed : 26.54 % Favored : 68.56 % 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: -0.29 (0.17), residues: 2450 helix: 0.65 (0.14), residues: 1351 sheet: 0.00 (0.60), residues: 87 loop : -1.34 (0.18), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 322 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 47 residues processed: 392 average time/residue: 1.5122 time to fit residues: 684.2166 Evaluate side-chains 330 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 283 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 33 residues processed: 16 average time/residue: 0.5373 time to fit residues: 15.9586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 275 GLN D 317 GLN ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN F 305 GLN ** O 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 HIS ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 28105 Z= 0.375 Angle : 0.656 10.940 39296 Z= 0.358 Chirality : 0.041 0.248 4343 Planarity : 0.005 0.066 3879 Dihedral : 27.549 178.394 5952 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.67 % Allowed : 26.18 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2450 helix: 0.53 (0.14), residues: 1361 sheet: -0.41 (0.57), residues: 84 loop : -1.30 (0.19), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 313 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 52 residues processed: 404 average time/residue: 1.5993 time to fit residues: 744.0298 Evaluate side-chains 329 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 277 time to evaluate : 2.949 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 40 residues processed: 14 average time/residue: 0.7991 time to fit residues: 18.3819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN O 39 HIS Q 38 ASN V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 314 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28105 Z= 0.225 Angle : 0.585 9.862 39296 Z= 0.321 Chirality : 0.037 0.247 4343 Planarity : 0.004 0.062 3879 Dihedral : 27.345 177.090 5952 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.54 % Allowed : 27.08 % Favored : 68.38 % 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: 2450 helix: 0.81 (0.14), residues: 1348 sheet: -0.79 (0.56), residues: 89 loop : -1.29 (0.19), residues: 1013 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 317 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 47 residues processed: 397 average time/residue: 1.4795 time to fit residues: 679.1486 Evaluate side-chains 333 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 286 time to evaluate : 2.828 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 41 residues processed: 8 average time/residue: 0.4689 time to fit residues: 9.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN F 305 GLN O 76 GLN Q 38 ASN S 108 ASN V 46 HIS V 60 ASN V 106 HIS ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 521 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28105 Z= 0.234 Angle : 0.592 13.284 39296 Z= 0.323 Chirality : 0.037 0.221 4343 Planarity : 0.004 0.058 3879 Dihedral : 27.288 176.991 5952 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.59 % Allowed : 27.22 % Favored : 68.20 % 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: -0.14 (0.17), residues: 2450 helix: 0.86 (0.14), residues: 1353 sheet: -0.92 (0.56), residues: 86 loop : -1.30 (0.19), residues: 1011 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 302 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 55 residues processed: 372 average time/residue: 1.5315 time to fit residues: 658.3287 Evaluate side-chains 339 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 40 residues processed: 16 average time/residue: 0.5267 time to fit residues: 15.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 149 optimal weight: 0.3980 chunk 192 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 221 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Q 38 ASN S 39 HIS U 38 ASN V 46 HIS V 60 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28105 Z= 0.208 Angle : 0.582 12.433 39296 Z= 0.318 Chirality : 0.037 0.179 4343 Planarity : 0.004 0.055 3879 Dihedral : 27.206 176.384 5952 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.69 % Allowed : 27.85 % Favored : 68.47 % 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: -0.04 (0.17), residues: 2450 helix: 0.96 (0.14), residues: 1352 sheet: -0.99 (0.55), residues: 86 loop : -1.28 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 299 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 44 residues processed: 366 average time/residue: 1.4793 time to fit residues: 634.2390 Evaluate side-chains 331 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 287 time to evaluate : 2.565 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 5 average time/residue: 0.3264 time to fit residues: 6.2726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN S 108 ASN U 38 ASN V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28105 Z= 0.285 Angle : 0.625 12.037 39296 Z= 0.337 Chirality : 0.039 0.291 4343 Planarity : 0.004 0.058 3879 Dihedral : 27.343 176.363 5952 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.87 % Allowed : 27.26 % Favored : 68.87 % 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: -0.12 (0.17), residues: 2450 helix: 0.85 (0.14), residues: 1357 sheet: -1.09 (0.56), residues: 76 loop : -1.26 (0.19), residues: 1017 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 294 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 47 residues processed: 360 average time/residue: 1.5059 time to fit residues: 626.5546 Evaluate side-chains 335 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 288 time to evaluate : 2.604 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 40 residues processed: 8 average time/residue: 0.6267 time to fit residues: 10.3793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 243 optimal weight: 0.0070 overall best weight: 0.6802 ------------------------------------------------------------------------------- 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN Q 38 ASN S 108 ASN U 38 ASN V 46 HIS V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28105 Z= 0.215 Angle : 0.606 12.223 39296 Z= 0.328 Chirality : 0.038 0.302 4343 Planarity : 0.004 0.059 3879 Dihedral : 27.253 175.933 5952 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.74 % Allowed : 28.79 % Favored : 68.47 % 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: -0.09 (0.17), residues: 2450 helix: 0.91 (0.14), residues: 1352 sheet: -1.15 (0.55), residues: 86 loop : -1.28 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 305 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 45 residues processed: 355 average time/residue: 1.5291 time to fit residues: 630.2098 Evaluate side-chains 329 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 284 time to evaluate : 2.439 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 40 residues processed: 5 average time/residue: 0.4459 time to fit residues: 6.4563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 249 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN O 76 GLN Q 38 ASN R 46 HIS ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN U 38 ASN V 60 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 ASN E 519 ASN E 521 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28105 Z= 0.359 Angle : 0.678 11.843 39296 Z= 0.365 Chirality : 0.042 0.279 4343 Planarity : 0.005 0.070 3879 Dihedral : 27.560 176.890 5952 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.74 % Allowed : 29.37 % Favored : 67.88 % 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: -0.29 (0.17), residues: 2450 helix: 0.67 (0.14), residues: 1366 sheet: -1.32 (0.57), residues: 75 loop : -1.27 (0.19), residues: 1009 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 293 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 41 residues processed: 345 average time/residue: 1.4862 time to fit residues: 594.7934 Evaluate side-chains 329 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 288 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 39 residues processed: 2 average time/residue: 0.3471 time to fit residues: 4.4726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 198 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 216 optimal weight: 0.7980 chunk 90 optimal weight: 0.0670 chunk 221 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN O 76 GLN Q 38 ASN R 46 HIS S 108 ASN V 46 HIS V 60 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.120779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086753 restraints weight = 55147.730| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.93 r_work: 0.3192 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28105 Z= 0.212 Angle : 0.630 13.086 39296 Z= 0.340 Chirality : 0.038 0.280 4343 Planarity : 0.004 0.076 3879 Dihedral : 27.322 176.267 5952 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.43 % Allowed : 30.09 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2450 helix: 0.78 (0.14), residues: 1359 sheet: -1.28 (0.57), residues: 75 loop : -1.30 (0.19), residues: 1016 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10862.53 seconds wall clock time: 194 minutes 35.65 seconds (11675.65 seconds total)