Starting phenix.real_space_refine on Sat Feb 17 21:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttc_26114/02_2024/7ttc_26114_trim_updated.pdb" } resolution = 3.6 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= 0.007 sd= 0.071 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 P 2 5.49 5 S 32 5.16 5 C 6441 2.51 5 N 1728 2.21 5 O 1996 1.98 5 H 9775 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 1267": "OE1" <-> "OE2" Residue "P PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19974 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 4853 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 8 Chain: "A" Number of atoms: 9259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9259 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 23, 'TRANS': 576} Chain breaks: 3 Chain: "E" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1324 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "D" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3356 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "P" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 462 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'TRANS': 27} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'K33': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.72, per 1000 atoms: 0.44 Number of scatterers: 19974 At special positions: 0 Unit cell: (105.234, 124.563, 137.449, 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) S 32 16.00 P 2 15.00 O 1996 8.00 N 1728 7.00 C 6441 6.00 H 9775 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.04 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: 15.70 Conformation dependent library (CDL) restraints added in 2.0 seconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 20.8% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.069A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.560A pdb=" N ARG A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.833A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 removed outlier: 3.772A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.974A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'E' and resid 40 through 45 removed outlier: 4.304A pdb=" N LYS E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 Processing helix chain 'D' and resid 34 through 44 Processing helix chain 'D' and resid 48 through 60 removed outlier: 3.828A pdb=" N ASP D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 105 through 119 removed outlier: 3.748A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 138 through 153 Processing helix chain 'D' and resid 160 through 188 removed outlier: 3.713A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 209 through 212 No H-bonds generated for 'chain 'D' and resid 209 through 212' Processing helix chain 'D' and resid 215 through 224 removed outlier: 3.609A pdb=" N ARG D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 240 Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing sheet with id= A, first strand: chain 'B' and resid 48 through 50 Processing sheet with id= B, first strand: chain 'B' and resid 66 through 68 Processing sheet with id= C, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.733A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.645A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.777A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.521A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.633A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.558A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 179 through 183 removed outlier: 3.865A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 321 through 328 removed outlier: 6.434A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.570A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 352 through 355 removed outlier: 8.569A pdb=" N ARG A 353 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 414 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLU A 355 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 416 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 425 through 430 removed outlier: 3.522A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 32 through 34 removed outlier: 5.961A pdb=" N ASN E 96 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU E 101 " --> pdb=" O ASN E 96 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'P' and resid 1295 through 1298 removed outlier: 3.683A pdb=" N VAL P1272 " --> pdb=" O ARG P1269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG P1269 " --> pdb=" O VAL P1272 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE P1274 " --> pdb=" O GLU P1267 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU P1267 " --> pdb=" O PHE P1274 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.36 Time building geometry restraints manager: 16.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9775 1.03 - 1.23: 786 1.23 - 1.43: 3805 1.43 - 1.63: 5763 1.63 - 1.83: 62 Bond restraints: 20191 Sorted by residual: bond pdb=" C34 K33 A 901 " pdb=" O35 K33 A 901 " ideal model delta sigma weight residual 1.301 1.430 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C93 K33 A 901 " pdb=" O94 K33 A 901 " ideal model delta sigma weight residual 1.473 1.361 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C36 K33 A 901 " pdb=" C37 K33 A 901 " ideal model delta sigma weight residual 1.504 1.607 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C34 K33 A 901 " pdb=" O83 K33 A 901 " ideal model delta sigma weight residual 1.544 1.473 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C ARG B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.333 1.302 0.032 1.01e-02 9.80e+03 9.86e+00 ... (remaining 20186 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.55: 227 105.55 - 112.70: 22628 112.70 - 119.85: 5674 119.85 - 126.99: 7584 126.99 - 134.14: 123 Bond angle restraints: 36236 Sorted by residual: angle pdb=" N ASN A 594 " pdb=" CA ASN A 594 " pdb=" C ASN A 594 " ideal model delta sigma weight residual 107.67 115.72 -8.05 2.09e+00 2.29e-01 1.48e+01 angle pdb=" N ASN A 448 " pdb=" CA ASN A 448 " pdb=" C ASN A 448 " ideal model delta sigma weight residual 107.93 102.56 5.37 1.65e+00 3.67e-01 1.06e+01 angle pdb=" N GLY D 153 " pdb=" CA GLY D 153 " pdb=" C GLY D 153 " ideal model delta sigma weight residual 112.77 116.93 -4.16 1.28e+00 6.10e-01 1.06e+01 angle pdb=" CB ARG D 188 " pdb=" CG ARG D 188 " pdb=" CD ARG D 188 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 angle pdb=" N PHE A 738 " pdb=" CA PHE A 738 " pdb=" C PHE A 738 " ideal model delta sigma weight residual 109.24 114.08 -4.84 1.51e+00 4.39e-01 1.03e+01 ... (remaining 36231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 9375 34.50 - 69.00: 209 69.00 - 103.50: 14 103.50 - 138.00: 6 138.00 - 172.50: 1 Dihedral angle restraints: 9605 sinusoidal: 5167 harmonic: 4438 Sorted by residual: dihedral pdb=" C34 K33 A 901 " pdb=" C36 K33 A 901 " pdb=" O35 K33 A 901 " pdb=" C37 K33 A 901 " ideal model delta sinusoidal sigma weight residual 260.53 88.03 172.50 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA PRO A 326 " pdb=" C PRO A 326 " pdb=" N GLU A 327 " pdb=" CA GLU A 327 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C21 K33 A 901 " pdb=" C22 K33 A 901 " pdb=" C23 K33 A 901 " pdb=" C24 K33 A 901 " ideal model delta sinusoidal sigma weight residual 207.92 82.17 125.75 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 9602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1159 0.059 - 0.118: 329 0.118 - 0.178: 51 0.178 - 0.237: 3 0.237 - 0.296: 1 Chirality restraints: 1543 Sorted by residual: chirality pdb=" C37 K33 A 901 " pdb=" C36 K33 A 901 " pdb=" C81 K33 A 901 " pdb=" O38 K33 A 901 " both_signs ideal model delta sigma weight residual False 2.55 2.85 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA TYR D 185 " pdb=" N TYR D 185 " pdb=" C TYR D 185 " pdb=" CB TYR D 185 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA GLN A 446 " pdb=" N GLN A 446 " pdb=" C GLN A 446 " pdb=" CB GLN A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1540 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 112 " -0.076 9.50e-02 1.11e+02 3.65e-02 1.62e+01 pdb=" NE ARG D 112 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 112 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG D 112 " 0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG D 112 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG D 112 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG D 112 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG D 112 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 112 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 547 " 0.071 9.50e-02 1.11e+02 3.48e-02 1.52e+01 pdb=" NE ARG A 547 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 547 " 0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG A 547 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG A 547 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 547 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG A 547 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 547 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 547 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 781 " 0.017 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C GLY A 781 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY A 781 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 782 " 0.019 2.00e-02 2.50e+03 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 524 2.13 - 2.75: 36476 2.75 - 3.36: 51831 3.36 - 3.98: 68400 3.98 - 4.60: 107299 Nonbonded interactions: 264530 Sorted by model distance: nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.512 1.850 nonbonded pdb=" O SER E 44 " pdb="HH12 ARG E 47 " model vdw 1.548 1.850 nonbonded pdb="HD22 ASN A 185 " pdb=" O PHE A 188 " model vdw 1.555 1.850 nonbonded pdb=" OD1 ASP D 93 " pdb="HH12 ARG D 112 " model vdw 1.557 1.850 nonbonded pdb=" OD2 ASP B 363 " pdb=" HH TYR B 388 " model vdw 1.568 1.850 ... (remaining 264525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.250 Extract box with map and model: 3.660 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 63.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.010 0.129 10416 Z= 0.629 Angle : 0.905 8.053 14143 Z= 0.540 Chirality : 0.054 0.296 1543 Planarity : 0.006 0.080 1845 Dihedral : 12.849 172.505 3748 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.00 (0.23), residues: 1262 helix: 0.39 (0.28), residues: 268 sheet: 1.00 (0.25), residues: 408 loop : 0.75 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP E 73 HIS 0.009 0.003 HIS B 64 PHE 0.025 0.003 PHE A 791 TYR 0.030 0.004 TYR D 77 ARG 0.064 0.005 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.410 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 ASN cc_start: 0.8446 (m-40) cc_final: 0.8136 (t0) REVERT: B 296 ILE cc_start: 0.8561 (mt) cc_final: 0.8232 (mt) REVERT: B 305 VAL cc_start: 0.9081 (t) cc_final: 0.8840 (p) REVERT: B 306 MET cc_start: 0.6787 (ppp) cc_final: 0.6516 (ppp) REVERT: B 369 THR cc_start: 0.6527 (m) cc_final: 0.6144 (m) REVERT: A 276 ASN cc_start: 0.8187 (t0) cc_final: 0.7982 (t0) REVERT: A 357 ASN cc_start: 0.8436 (t0) cc_final: 0.8102 (t0) REVERT: D 111 MET cc_start: 0.8769 (mmm) cc_final: 0.8549 (tpt) REVERT: D 172 ASP cc_start: 0.8528 (t70) cc_final: 0.8229 (t0) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.6158 time to fit residues: 246.8861 Evaluate side-chains 202 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 ASN P1271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10416 Z= 0.149 Angle : 0.532 5.771 14143 Z= 0.287 Chirality : 0.043 0.146 1543 Planarity : 0.004 0.047 1845 Dihedral : 9.672 164.727 1443 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.93 % Allowed : 6.76 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1262 helix: 1.97 (0.31), residues: 270 sheet: 0.73 (0.25), residues: 408 loop : 0.88 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 546 HIS 0.002 0.001 HIS A 533 PHE 0.019 0.001 PHE A 440 TYR 0.012 0.001 TYR D 79 ARG 0.004 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 1.415 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 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 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: B 287 ASN cc_start: 0.8831 (m-40) cc_final: 0.8625 (t0) REVERT: B 296 ILE cc_start: 0.8595 (mt) cc_final: 0.8319 (mt) REVERT: B 306 MET cc_start: 0.6682 (ppp) cc_final: 0.6385 (ppp) REVERT: B 331 VAL cc_start: 0.7126 (p) cc_final: 0.6633 (m) REVERT: A 303 LYS cc_start: 0.8441 (tptp) cc_final: 0.8178 (tmtt) REVERT: A 738 PHE cc_start: 0.8692 (p90) cc_final: 0.8426 (p90) REVERT: D 172 ASP cc_start: 0.8277 (t70) cc_final: 0.7976 (t0) outliers start: 10 outliers final: 8 residues processed: 211 average time/residue: 0.5639 time to fit residues: 159.7454 Evaluate side-chains 190 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10416 Z= 0.166 Angle : 0.488 4.372 14143 Z= 0.262 Chirality : 0.042 0.144 1543 Planarity : 0.003 0.039 1845 Dihedral : 8.891 171.183 1443 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.93 % Allowed : 8.61 % Favored : 90.46 % 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: 1.41 (0.24), residues: 1262 helix: 2.22 (0.31), residues: 271 sheet: 0.32 (0.24), residues: 427 loop : 1.00 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 546 HIS 0.004 0.001 HIS B 121 PHE 0.017 0.001 PHE A 440 TYR 0.017 0.001 TYR B 345 ARG 0.004 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.568 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 ASN cc_start: 0.8963 (m-40) cc_final: 0.8726 (t0) REVERT: B 296 ILE cc_start: 0.8618 (mt) cc_final: 0.8359 (mt) REVERT: B 306 MET cc_start: 0.6577 (ppp) cc_final: 0.6252 (ppp) REVERT: A 239 ASN cc_start: 0.7896 (t0) cc_final: 0.7145 (p0) REVERT: A 303 LYS cc_start: 0.8482 (tptp) cc_final: 0.8262 (tmtt) REVERT: D 111 MET cc_start: 0.8833 (mmm) cc_final: 0.8445 (tpt) REVERT: D 172 ASP cc_start: 0.8269 (t70) cc_final: 0.7992 (t0) outliers start: 10 outliers final: 8 residues processed: 204 average time/residue: 0.5491 time to fit residues: 151.1778 Evaluate side-chains 193 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 122 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10416 Z= 0.191 Angle : 0.478 5.431 14143 Z= 0.254 Chirality : 0.042 0.135 1543 Planarity : 0.003 0.036 1845 Dihedral : 8.703 171.720 1443 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.11 % Allowed : 9.17 % Favored : 89.72 % 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: 1.33 (0.24), residues: 1262 helix: 2.25 (0.31), residues: 271 sheet: 0.25 (0.24), residues: 428 loop : 0.91 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 745 HIS 0.004 0.001 HIS A 186 PHE 0.022 0.001 PHE A 197 TYR 0.013 0.001 TYR D 79 ARG 0.005 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 1.548 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 MET cc_start: 0.8027 (tmm) cc_final: 0.7534 (tmm) REVERT: B 287 ASN cc_start: 0.9052 (m-40) cc_final: 0.8842 (t0) REVERT: B 296 ILE cc_start: 0.8643 (mt) cc_final: 0.8376 (mt) REVERT: B 306 MET cc_start: 0.6571 (ppp) cc_final: 0.6197 (ppp) REVERT: A 239 ASN cc_start: 0.7955 (t0) cc_final: 0.7233 (p0) REVERT: A 314 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8107 (mtm110) REVERT: A 338 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7439 (ttm110) REVERT: A 661 ARG cc_start: 0.7186 (mtt90) cc_final: 0.6877 (mtt90) REVERT: D 111 MET cc_start: 0.8876 (mmm) cc_final: 0.8503 (tpt) outliers start: 12 outliers final: 10 residues processed: 202 average time/residue: 0.5659 time to fit residues: 153.0413 Evaluate side-chains 190 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain P residue 1271 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10416 Z= 0.386 Angle : 0.559 5.893 14143 Z= 0.303 Chirality : 0.043 0.145 1543 Planarity : 0.004 0.038 1845 Dihedral : 8.728 170.323 1443 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.31 % Allowed : 9.26 % Favored : 88.43 % 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: 0.83 (0.23), residues: 1262 helix: 1.79 (0.30), residues: 268 sheet: 0.07 (0.23), residues: 418 loop : 0.50 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 228 HIS 0.008 0.001 HIS A 186 PHE 0.019 0.002 PHE A 791 TYR 0.015 0.002 TYR D 79 ARG 0.006 0.001 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 1.725 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 LEU cc_start: 0.8082 (tp) cc_final: 0.7860 (tp) REVERT: B 226 MET cc_start: 0.8049 (tmm) cc_final: 0.7591 (tmm) REVERT: B 296 ILE cc_start: 0.8680 (mt) cc_final: 0.8452 (mt) REVERT: A 239 ASN cc_start: 0.8155 (t0) cc_final: 0.7417 (p0) REVERT: A 314 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8078 (mtm110) REVERT: A 338 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7442 (ttm110) outliers start: 25 outliers final: 19 residues processed: 204 average time/residue: 0.5857 time to fit residues: 160.8940 Evaluate side-chains 204 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain P residue 1271 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10416 Z= 0.141 Angle : 0.466 5.156 14143 Z= 0.246 Chirality : 0.042 0.135 1543 Planarity : 0.004 0.043 1845 Dihedral : 8.519 172.418 1443 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.02 % Allowed : 10.83 % Favored : 88.15 % 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: 1.14 (0.23), residues: 1262 helix: 2.15 (0.31), residues: 269 sheet: 0.17 (0.23), residues: 424 loop : 0.73 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 745 HIS 0.007 0.001 HIS B 121 PHE 0.015 0.001 PHE A 440 TYR 0.013 0.001 TYR D 79 ARG 0.007 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 1.650 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 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 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: B 67 LEU cc_start: 0.7992 (tp) cc_final: 0.7776 (tp) REVERT: B 146 LYS cc_start: 0.8652 (tptp) cc_final: 0.8420 (tptp) REVERT: B 226 MET cc_start: 0.7992 (tmm) cc_final: 0.7522 (tmm) REVERT: B 296 ILE cc_start: 0.8621 (mt) cc_final: 0.8410 (mt) REVERT: B 306 MET cc_start: 0.6505 (ppp) cc_final: 0.6178 (ppp) REVERT: A 239 ASN cc_start: 0.8122 (t0) cc_final: 0.7410 (p0) REVERT: A 306 ASP cc_start: 0.8494 (t70) cc_final: 0.8286 (t70) REVERT: A 661 ARG cc_start: 0.7221 (mtt90) cc_final: 0.6962 (mtt90) outliers start: 11 outliers final: 9 residues processed: 201 average time/residue: 0.5813 time to fit residues: 158.9996 Evaluate side-chains 191 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10416 Z= 0.164 Angle : 0.470 6.809 14143 Z= 0.247 Chirality : 0.041 0.132 1543 Planarity : 0.003 0.036 1845 Dihedral : 8.460 172.593 1443 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.02 % Allowed : 11.30 % Favored : 87.69 % 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: 1.13 (0.23), residues: 1262 helix: 2.10 (0.31), residues: 274 sheet: 0.18 (0.23), residues: 423 loop : 0.72 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 745 HIS 0.007 0.001 HIS B 121 PHE 0.014 0.001 PHE A 440 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 1.816 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 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 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: B 67 LEU cc_start: 0.7982 (tp) cc_final: 0.7763 (tp) REVERT: B 146 LYS cc_start: 0.8666 (tptp) cc_final: 0.8454 (tptp) REVERT: B 226 MET cc_start: 0.7979 (tmm) cc_final: 0.7508 (tmm) REVERT: A 239 ASN cc_start: 0.8129 (t0) cc_final: 0.7420 (p0) REVERT: A 295 LEU cc_start: 0.8717 (tt) cc_final: 0.8324 (tt) REVERT: A 306 ASP cc_start: 0.8532 (t70) cc_final: 0.8327 (t70) REVERT: A 314 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8048 (mtm110) REVERT: A 661 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6895 (mtt90) outliers start: 11 outliers final: 6 residues processed: 197 average time/residue: 0.5775 time to fit residues: 153.5001 Evaluate side-chains 186 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10416 Z= 0.185 Angle : 0.471 6.263 14143 Z= 0.248 Chirality : 0.041 0.135 1543 Planarity : 0.003 0.036 1845 Dihedral : 8.361 172.676 1443 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.02 % Allowed : 11.30 % Favored : 87.69 % 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: 1.22 (0.24), residues: 1262 helix: 2.33 (0.32), residues: 267 sheet: 0.22 (0.24), residues: 423 loop : 0.72 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 745 HIS 0.005 0.001 HIS A 186 PHE 0.013 0.001 PHE A 440 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 1.849 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 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 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: B 67 LEU cc_start: 0.7993 (tp) cc_final: 0.7792 (tp) REVERT: B 146 LYS cc_start: 0.8660 (tptp) cc_final: 0.8450 (tptp) REVERT: B 226 MET cc_start: 0.7959 (tmm) cc_final: 0.7488 (tmm) REVERT: A 239 ASN cc_start: 0.8163 (t0) cc_final: 0.7405 (p0) REVERT: A 306 ASP cc_start: 0.8508 (t70) cc_final: 0.8306 (t70) REVERT: A 314 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7987 (mtm110) REVERT: A 661 ARG cc_start: 0.7179 (mtt90) cc_final: 0.6866 (mtt90) outliers start: 11 outliers final: 9 residues processed: 193 average time/residue: 0.5562 time to fit residues: 144.5691 Evaluate side-chains 194 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain P residue 1271 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10416 Z= 0.143 Angle : 0.461 7.127 14143 Z= 0.242 Chirality : 0.041 0.131 1543 Planarity : 0.003 0.035 1845 Dihedral : 8.327 173.127 1443 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.65 % Allowed : 11.85 % Favored : 87.50 % 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: 1.28 (0.24), residues: 1262 helix: 2.31 (0.32), residues: 273 sheet: 0.28 (0.24), residues: 422 loop : 0.76 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.005 0.001 HIS A 186 PHE 0.015 0.001 PHE A 440 TYR 0.013 0.001 TYR D 184 ARG 0.008 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 1.568 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 LYS cc_start: 0.8652 (tptp) cc_final: 0.8441 (tptp) REVERT: B 226 MET cc_start: 0.7951 (tmm) cc_final: 0.7442 (tmm) REVERT: A 239 ASN cc_start: 0.8149 (t0) cc_final: 0.7419 (p0) REVERT: A 306 ASP cc_start: 0.8493 (t70) cc_final: 0.8038 (t70) REVERT: A 314 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8108 (mtm110) REVERT: A 661 ARG cc_start: 0.7117 (mtt90) cc_final: 0.6811 (mtt90) outliers start: 7 outliers final: 6 residues processed: 194 average time/residue: 0.5537 time to fit residues: 145.0645 Evaluate side-chains 185 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10416 Z= 0.164 Angle : 0.465 5.728 14143 Z= 0.244 Chirality : 0.041 0.132 1543 Planarity : 0.003 0.036 1845 Dihedral : 8.258 173.277 1443 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.74 % Allowed : 11.76 % Favored : 87.50 % 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: 1.31 (0.24), residues: 1262 helix: 2.45 (0.32), residues: 267 sheet: 0.29 (0.24), residues: 422 loop : 0.74 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.005 0.001 HIS A 186 PHE 0.015 0.001 PHE A 440 TYR 0.013 0.001 TYR D 184 ARG 0.006 0.000 ARG D 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.692 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 THR cc_start: 0.7955 (t) cc_final: 0.7677 (t) REVERT: B 226 MET cc_start: 0.7978 (tmm) cc_final: 0.7487 (tmm) REVERT: B 306 MET cc_start: 0.6346 (ppp) cc_final: 0.6009 (ppp) REVERT: A 239 ASN cc_start: 0.8165 (t0) cc_final: 0.7430 (p0) REVERT: A 314 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8062 (mtm110) REVERT: A 661 ARG cc_start: 0.7156 (mtt90) cc_final: 0.6826 (mtt90) outliers start: 8 outliers final: 6 residues processed: 191 average time/residue: 0.5802 time to fit residues: 148.7854 Evaluate side-chains 189 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.185092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131879 restraints weight = 42951.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134450 restraints weight = 19572.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133330 restraints weight = 13724.950| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10416 Z= 0.218 Angle : 0.500 10.167 14143 Z= 0.265 Chirality : 0.042 0.229 1543 Planarity : 0.004 0.050 1845 Dihedral : 8.292 172.861 1443 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.83 % Allowed : 11.94 % Favored : 87.22 % 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: 1.22 (0.24), residues: 1262 helix: 2.35 (0.32), residues: 267 sheet: 0.26 (0.24), residues: 422 loop : 0.68 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.005 0.001 HIS A 186 PHE 0.013 0.001 PHE A 440 TYR 0.013 0.001 TYR P1298 ARG 0.010 0.000 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4626.24 seconds wall clock time: 82 minutes 26.90 seconds (4946.90 seconds total)