Starting phenix.real_space_refine on Sat Feb 17 16:00:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf5_29978/02_2024/8gf5_29978_trim_updated.pdb" } resolution = 3.0 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= -0.001 sd= 0.089 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 Ni 1 6.56 5 P 1 5.49 5 S 120 5.16 5 C 11981 2.51 5 N 3320 2.21 5 O 3704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B GLU 548": "OE1" <-> "OE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ASP 296": "OD1" <-> "OD2" Residue "D ARG 320": "NH1" <-> "NH2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 381": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 398": "OD1" <-> "OD2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E ASP 166": "OD1" <-> "OD2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 225": "OD1" <-> "OD2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ASP 166": "OD1" <-> "OD2" Residue "F ASP 171": "OD1" <-> "OD2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "X ASP 10": "OD1" <-> "OD2" Residue "X PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 76": "OD1" <-> "OD2" Residue "X GLU 80": "OE1" <-> "OE2" Residue "X PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 123": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19127 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4282 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 22, 'TRANS': 537} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3682 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3133 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 417} Chain: "D" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3143 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 419} Chain: "E" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "F" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "X" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'COM': 1, 'F43': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Classifications: {'peptide': 1} Time building chain proxies: 10.60, per 1000 atoms: 0.55 Number of scatterers: 19127 At special positions: 0 Unit cell: (98.12, 102.58, 137.145, 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) Ni 1 28.00 S 120 16.00 P 1 15.00 O 3704 8.00 N 3320 7.00 C 11981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.80 Conformation dependent library (CDL) restraints added in 3.2 seconds 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 13 sheets defined 46.8% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 48 through 63 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.877A pdb=" N TRP A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.719A pdb=" N HIS A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.644A pdb=" N ASP A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 189' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 198 through 201 No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 234 through 252 removed outlier: 4.035A pdb=" N SER A 238 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.927A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 313 through 329 Processing helix chain 'A' and resid 332 through 335 No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 344 through 350 removed outlier: 4.003A pdb=" N ALA A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 387 through 407 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 437 Processing helix chain 'A' and resid 440 through 458 Processing helix chain 'A' and resid 470 through 473 removed outlier: 3.660A pdb=" N GLY A 473 " --> pdb=" O ASP A 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 470 through 473' Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.568A pdb=" N HIS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 140 through 153 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 198 through 201 No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 234 through 252 removed outlier: 3.708A pdb=" N THR B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER B 238 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 313 through 329 removed outlier: 3.694A pdb=" N ALA B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 419 through 437 Processing helix chain 'B' and resid 440 through 458 Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 505 through 517 removed outlier: 3.845A pdb=" N HIS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 115 through 119 Processing helix chain 'C' and resid 124 through 142 removed outlier: 3.519A pdb=" N THR C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C 142 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.722A pdb=" N ALA C 150 " --> pdb=" O MET C 147 " (cutoff:3.500A) Proline residue: C 151 - end of helix removed outlier: 3.672A pdb=" N ALA C 156 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 158 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 187 through 190 Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.711A pdb=" N ALA C 210 " --> pdb=" O MET C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.755A pdb=" N LEU C 236 " --> pdb=" O HIS C 233 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 241 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 removed outlier: 6.086A pdb=" N VAL C 249 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 250 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 276 Processing helix chain 'C' and resid 297 through 318 Processing helix chain 'C' and resid 322 through 340 removed outlier: 3.511A pdb=" N VAL C 325 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 326 " --> pdb=" O GLN C 323 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 332 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 340 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 360 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 388 through 396 Processing helix chain 'C' and resid 406 through 419 removed outlier: 6.938A pdb=" N LEU C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'D' and resid 21 through 24 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.503A pdb=" N ALA D 79 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASP D 80 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 90 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 124 through 142 removed outlier: 3.598A pdb=" N ALA D 127 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 130 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 205 through 222 Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 245 through 255 removed outlier: 5.811A pdb=" N VAL D 249 " --> pdb=" O ASN D 246 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP D 251 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 297 through 317 Processing helix chain 'D' and resid 325 through 340 removed outlier: 4.351A pdb=" N LEU D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 361 removed outlier: 6.158A pdb=" N VAL D 350 " --> pdb=" O TYR D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 406 through 418 removed outlier: 7.132A pdb=" N LEU D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'E' and resid 13 through 23 Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 75 through 78 No H-bonds generated for 'chain 'E' and resid 75 through 78' Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 128 through 140 Processing helix chain 'E' and resid 206 through 212 Processing helix chain 'E' and resid 227 through 245 Processing helix chain 'F' and resid 13 through 23 Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 57 through 60 No H-bonds generated for 'chain 'F' and resid 57 through 60' Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 75 through 78 No H-bonds generated for 'chain 'F' and resid 75 through 78' Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 128 through 140 Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 227 through 245 Processing helix chain 'X' and resid 24 through 34 Processing helix chain 'X' and resid 95 through 108 removed outlier: 3.713A pdb=" N LYS X 100 " --> pdb=" O GLU X 96 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS X 107 " --> pdb=" O SER X 103 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 118 through 122 Processing sheet with id= B, first strand: chain 'B' and resid 274 through 276 Processing sheet with id= C, first strand: chain 'C' and resid 172 through 174 removed outlier: 3.524A pdb=" N SER C 108 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 279 through 284 removed outlier: 7.013A pdb=" N PHE C 291 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.667A pdb=" N SER D 108 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 99 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 279 through 281 Processing sheet with id= G, first strand: chain 'E' and resid 83 through 88 Processing sheet with id= H, first strand: chain 'E' and resid 176 through 179 Processing sheet with id= I, first strand: chain 'F' and resid 83 through 88 removed outlier: 3.513A pdb=" N PHE F 88 " --> pdb=" O GLN F 122 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 125 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 176 through 179 Processing sheet with id= K, first strand: chain 'X' and resid 14 through 18 removed outlier: 3.930A pdb=" N GLU X 15 " --> pdb=" O ARG X 116 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG X 116 " --> pdb=" O GLU X 15 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'X' and resid 71 through 74 Processing sheet with id= M, first strand: chain 'X' and resid 44 through 49 removed outlier: 5.708A pdb=" N VAL X 85 " --> pdb=" O PRO X 48 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 8.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 7441 1.38 - 1.56: 11835 1.56 - 1.74: 2 1.74 - 1.92: 210 1.92 - 2.10: 4 Bond restraints: 19492 Sorted by residual: bond pdb=" C1 TP7 B 601 " pdb=" O1 TP7 B 601 " ideal model delta sigma weight residual 1.185 1.430 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" CA ASN A 151 " pdb=" C ASN A 151 " ideal model delta sigma weight residual 1.522 1.472 0.051 1.36e-02 5.41e+03 1.39e+01 bond pdb=" CA GLU B 484 " pdb=" C GLU B 484 " ideal model delta sigma weight residual 1.520 1.477 0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" N PHE B 466 " pdb=" CA PHE B 466 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" CA AGM A 285 " pdb=" C AGM A 285 " ideal model delta sigma weight residual 1.525 1.455 0.070 2.10e-02 2.27e+03 1.12e+01 ... (remaining 19487 not shown) Histogram of bond angle deviations from ideal: 84.78 - 101.97: 101 101.97 - 119.17: 15966 119.17 - 136.36: 10339 136.36 - 153.55: 0 153.55 - 170.74: 2 Bond angle restraints: 26408 Sorted by residual: angle pdb=" N LEU A 486 " pdb=" CA LEU A 486 " pdb=" C LEU A 486 " ideal model delta sigma weight residual 108.22 97.25 10.97 9.00e-01 1.23e+00 1.49e+02 angle pdb=" N GLY A 482 " pdb=" CA GLY A 482 " pdb=" C GLY A 482 " ideal model delta sigma weight residual 112.50 121.07 -8.57 1.16e+00 7.43e-01 5.45e+01 angle pdb=" N PHE A 466 " pdb=" CA PHE A 466 " pdb=" C PHE A 466 " ideal model delta sigma weight residual 113.50 104.58 8.92 1.23e+00 6.61e-01 5.26e+01 angle pdb=" N ALA A 283 " pdb=" CA ALA A 283 " pdb=" C ALA A 283 " ideal model delta sigma weight residual 111.07 118.69 -7.62 1.07e+00 8.73e-01 5.08e+01 angle pdb=" N ASN A 151 " pdb=" CA ASN A 151 " pdb=" C ASN A 151 " ideal model delta sigma weight residual 111.71 119.51 -7.80 1.15e+00 7.56e-01 4.60e+01 ... (remaining 26403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10641 17.57 - 35.15: 844 35.15 - 52.72: 126 52.72 - 70.30: 25 70.30 - 87.87: 25 Dihedral angle restraints: 11661 sinusoidal: 4535 harmonic: 7126 Sorted by residual: dihedral pdb=" C HIS A 152 " pdb=" N HIS A 152 " pdb=" CA HIS A 152 " pdb=" CB HIS A 152 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" N HIS A 152 " pdb=" C HIS A 152 " pdb=" CA HIS A 152 " pdb=" CB HIS A 152 " ideal model delta harmonic sigma weight residual 122.80 136.49 -13.69 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" CA ASP C 346 " pdb=" C ASP C 346 " pdb=" N TYR C 347 " pdb=" CA TYR C 347 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 11658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.987: 2907 0.987 - 1.973: 0 1.973 - 2.960: 0 2.960 - 3.947: 0 3.947 - 4.933: 1 Chirality restraints: 2908 Sorted by residual: chirality pdb=" CA TP7 B 601 " pdb=" N TP7 B 601 " pdb=" C TP7 B 601 " pdb=" CB TP7 B 601 " both_signs ideal model delta sigma weight residual False -2.60 2.33 -4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" CA HIS A 152 " pdb=" N HIS A 152 " pdb=" C HIS A 152 " pdb=" CB HIS A 152 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ASN A 151 " pdb=" N ASN A 151 " pdb=" C ASN A 151 " pdb=" CB ASN A 151 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 2905 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB F43 A 602 " -0.146 2.00e-02 2.50e+03 1.85e-01 5.12e+02 pdb=" C1B F43 A 602 " -0.155 2.00e-02 2.50e+03 pdb=" C3B F43 A 602 " 0.288 2.00e-02 2.50e+03 pdb=" C4B F43 A 602 " -0.029 2.00e-02 2.50e+03 pdb=" CHC F43 A 602 " -0.172 2.00e-02 2.50e+03 pdb="NI F43 A 602 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TP7 B 601 " -0.096 2.00e-02 2.50e+03 1.80e-01 4.06e+02 pdb=" CA TP7 B 601 " -0.017 2.00e-02 2.50e+03 pdb=" C1 TP7 B 601 " 0.352 2.00e-02 2.50e+03 pdb=" C2 TP7 B 601 " -0.126 2.00e-02 2.50e+03 pdb=" O1 TP7 B 601 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND F43 A 602 " -0.064 2.00e-02 2.50e+03 1.26e-01 2.38e+02 pdb=" C1D F43 A 602 " -0.084 2.00e-02 2.50e+03 pdb=" C2D F43 A 602 " 0.211 2.00e-02 2.50e+03 pdb=" C4D F43 A 602 " -0.127 2.00e-02 2.50e+03 pdb=" CHD F43 A 602 " -0.072 2.00e-02 2.50e+03 pdb="NI F43 A 602 " 0.135 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 273 2.59 - 3.17: 18106 3.17 - 3.74: 31612 3.74 - 4.32: 47168 4.32 - 4.90: 78087 Nonbonded interactions: 175246 Sorted by model distance: nonbonded pdb=" OG SER E 52 " pdb=" O HIS E 54 " model vdw 2.010 2.440 nonbonded pdb=" O ASN D 374 " pdb=" OG1 THR D 380 " model vdw 2.071 2.440 nonbonded pdb=" O ARG F 19 " pdb=" OG SER F 23 " model vdw 2.076 2.440 nonbonded pdb=" OD2 ASP A 174 " pdb=" OG1 THR A 226 " model vdw 2.084 2.440 nonbonded pdb=" OE2 GLU A 131 " pdb=" N VAL A 138 " model vdw 2.100 2.520 ... (remaining 175241 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 'C' selection = (chain 'D' and resid 3 through 431) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.470 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: 3.450 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 52.710 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.006 0.245 19492 Z= 0.413 Angle : 0.747 11.093 26408 Z= 0.444 Chirality : 0.105 4.933 2908 Planarity : 0.008 0.185 3486 Dihedral : 13.517 87.871 7133 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 0.61 % Favored : 99.29 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.98 % 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: -0.26 (0.17), residues: 2479 helix: 0.57 (0.15), residues: 1223 sheet: -0.54 (0.48), residues: 124 loop : -0.91 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 240 HIS 0.008 0.002 HIS B 454 PHE 0.025 0.002 PHE A 463 TYR 0.030 0.002 TYR A 336 ARG 0.006 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: E 100 TYR cc_start: 0.8064 (m-80) cc_final: 0.7783 (m-80) REVERT: F 60 MET cc_start: 0.8516 (ttt) cc_final: 0.8211 (ttm) outliers start: 2 outliers final: 1 residues processed: 196 average time/residue: 1.4843 time to fit residues: 325.0958 Evaluate side-chains 123 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 330 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN F 54 HIS F 138 GLN X 13 GLN X 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 19492 Z= 0.375 Angle : 0.656 13.784 26408 Z= 0.340 Chirality : 0.092 4.305 2908 Planarity : 0.005 0.076 3486 Dihedral : 5.834 65.447 2808 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.73 % Allowed : 8.31 % Favored : 89.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.98 % 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: 2479 helix: 0.47 (0.15), residues: 1248 sheet: -0.36 (0.49), residues: 118 loop : -0.73 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 447 HIS 0.006 0.001 HIS A 127 PHE 0.022 0.002 PHE C 332 TYR 0.022 0.002 TYR A 336 ARG 0.004 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8616 (mmp) cc_final: 0.8270 (mmp) REVERT: B 280 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7872 (ptm) outliers start: 34 outliers final: 15 residues processed: 150 average time/residue: 1.4007 time to fit residues: 237.3178 Evaluate side-chains 133 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 60 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 123 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19492 Z= 0.286 Angle : 0.587 15.322 26408 Z= 0.300 Chirality : 0.091 4.317 2908 Planarity : 0.005 0.072 3486 Dihedral : 5.592 64.363 2806 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.14 % Allowed : 10.05 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -0.08 (0.17), residues: 2479 helix: 0.51 (0.15), residues: 1248 sheet: -0.43 (0.51), residues: 113 loop : -0.56 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 447 HIS 0.005 0.001 HIS A 127 PHE 0.019 0.002 PHE C 332 TYR 0.016 0.001 TYR C 331 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8305 (tptt) REVERT: C 59 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7707 (ptm) REVERT: D 223 MET cc_start: 0.8318 (mtp) cc_final: 0.8074 (mtm) REVERT: X 29 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8365 (ptpt) outliers start: 42 outliers final: 17 residues processed: 156 average time/residue: 1.3757 time to fit residues: 242.6434 Evaluate side-chains 135 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 192 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19492 Z= 0.352 Angle : 0.608 14.496 26408 Z= 0.310 Chirality : 0.091 4.325 2908 Planarity : 0.005 0.067 3486 Dihedral : 5.567 63.928 2806 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.45 % Allowed : 11.73 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -0.02 (0.17), residues: 2479 helix: 0.59 (0.15), residues: 1233 sheet: -0.42 (0.50), residues: 113 loop : -0.55 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 447 HIS 0.006 0.001 HIS A 127 PHE 0.020 0.002 PHE X 111 TYR 0.022 0.002 TYR E 100 ARG 0.002 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 122 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8302 (tptt) REVERT: A 125 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8108 (tmm) REVERT: A 291 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: B 83 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5968 (pp) REVERT: F 185 MET cc_start: 0.8078 (ttt) cc_final: 0.7859 (ttt) outliers start: 48 outliers final: 17 residues processed: 150 average time/residue: 1.4094 time to fit residues: 238.3298 Evaluate side-chains 133 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 192 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19492 Z= 0.211 Angle : 0.564 16.318 26408 Z= 0.282 Chirality : 0.090 4.308 2908 Planarity : 0.004 0.064 3486 Dihedral : 5.316 62.501 2806 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.14 % Allowed : 13.41 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2479 helix: 0.70 (0.15), residues: 1251 sheet: -0.49 (0.50), residues: 115 loop : -0.40 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 447 HIS 0.006 0.001 HIS B 454 PHE 0.025 0.001 PHE X 111 TYR 0.022 0.001 TYR E 100 ARG 0.002 0.000 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8235 (tptt) REVERT: A 243 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6979 (ptt) REVERT: A 291 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: B 280 MET cc_start: 0.8569 (ppp) cc_final: 0.8327 (ptm) REVERT: C 125 MET cc_start: 0.8619 (mmm) cc_final: 0.8326 (mmp) outliers start: 42 outliers final: 15 residues processed: 162 average time/residue: 1.4473 time to fit residues: 263.6414 Evaluate side-chains 135 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 123 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19492 Z= 0.297 Angle : 0.597 15.013 26408 Z= 0.299 Chirality : 0.091 4.321 2908 Planarity : 0.004 0.065 3486 Dihedral : 5.366 62.900 2806 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.89 % Allowed : 14.38 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 2479 helix: 0.76 (0.15), residues: 1240 sheet: -0.45 (0.50), residues: 115 loop : -0.40 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.005 0.001 HIS B 454 PHE 0.027 0.002 PHE X 111 TYR 0.023 0.001 TYR E 100 ARG 0.005 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8305 (tptt) REVERT: A 291 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 280 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8321 (ptt) outliers start: 37 outliers final: 15 residues processed: 147 average time/residue: 1.4094 time to fit residues: 233.4764 Evaluate side-chains 131 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 123 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 201 optimal weight: 0.0770 chunk 133 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19492 Z= 0.151 Angle : 0.561 17.065 26408 Z= 0.277 Chirality : 0.090 4.300 2908 Planarity : 0.004 0.061 3486 Dihedral : 5.089 63.704 2806 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.48 % Allowed : 14.74 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: 2479 helix: 0.92 (0.16), residues: 1241 sheet: -0.43 (0.53), residues: 109 loop : -0.33 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 447 HIS 0.006 0.001 HIS B 454 PHE 0.034 0.001 PHE X 111 TYR 0.017 0.001 TYR E 100 ARG 0.004 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.7222 (ptm) cc_final: 0.7017 (ptt) REVERT: A 291 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: B 280 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8333 (ptm) REVERT: B 470 ASP cc_start: 0.7614 (m-30) cc_final: 0.7412 (m-30) outliers start: 29 outliers final: 10 residues processed: 156 average time/residue: 1.3305 time to fit residues: 235.6881 Evaluate side-chains 132 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.0570 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19492 Z= 0.164 Angle : 0.569 13.060 26408 Z= 0.280 Chirality : 0.090 4.333 2908 Planarity : 0.004 0.057 3486 Dihedral : 5.192 83.637 2806 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.53 % Allowed : 15.60 % Favored : 82.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2479 helix: 1.02 (0.16), residues: 1235 sheet: -0.38 (0.52), residues: 109 loop : -0.29 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 447 HIS 0.006 0.001 HIS B 454 PHE 0.030 0.001 PHE X 111 TYR 0.015 0.001 TYR E 100 ARG 0.008 0.000 ARG X 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.7213 (ptm) cc_final: 0.6996 (ptt) REVERT: B 280 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8347 (ptm) outliers start: 30 outliers final: 12 residues processed: 146 average time/residue: 1.3499 time to fit residues: 223.7290 Evaluate side-chains 130 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain F residue 123 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 201 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 146 optimal weight: 0.3980 overall best weight: 1.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19492 Z= 0.180 Angle : 0.575 12.400 26408 Z= 0.283 Chirality : 0.091 4.351 2908 Planarity : 0.004 0.053 3486 Dihedral : 5.219 86.643 2806 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.38 % Allowed : 15.66 % Favored : 82.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2479 helix: 1.05 (0.16), residues: 1236 sheet: -0.09 (0.50), residues: 119 loop : -0.31 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 447 HIS 0.005 0.001 HIS B 454 PHE 0.028 0.001 PHE X 111 TYR 0.029 0.001 TYR B 102 ARG 0.003 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8235 (tptt) REVERT: A 72 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7095 (mmm) REVERT: A 243 MET cc_start: 0.7238 (ptm) cc_final: 0.7002 (ptt) REVERT: F 185 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7696 (ttt) outliers start: 27 outliers final: 16 residues processed: 140 average time/residue: 1.4282 time to fit residues: 225.5872 Evaluate side-chains 134 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 185 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19492 Z= 0.224 Angle : 0.598 14.947 26408 Z= 0.293 Chirality : 0.091 4.362 2908 Planarity : 0.004 0.055 3486 Dihedral : 5.353 94.030 2806 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.17 % Allowed : 15.86 % Favored : 82.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.98 % 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: 0.51 (0.17), residues: 2479 helix: 1.05 (0.16), residues: 1235 sheet: -0.11 (0.50), residues: 119 loop : -0.32 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.006 0.001 HIS B 454 PHE 0.025 0.001 PHE X 111 TYR 0.017 0.001 TYR E 100 ARG 0.004 0.000 ARG D 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8213 (tptt) REVERT: A 72 MET cc_start: 0.7390 (mtp) cc_final: 0.6954 (mmm) REVERT: A 243 MET cc_start: 0.7248 (ptm) cc_final: 0.7019 (ptt) REVERT: C 125 MET cc_start: 0.8542 (mmm) cc_final: 0.8136 (mmp) REVERT: F 185 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7666 (ttt) REVERT: X 100 LYS cc_start: 0.8656 (ptpp) cc_final: 0.8361 (ptpp) outliers start: 23 outliers final: 14 residues processed: 134 average time/residue: 1.3475 time to fit residues: 205.5684 Evaluate side-chains 132 residues out of total 1961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 185 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057237 restraints weight = 59347.968| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.01 r_work: 0.2865 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19492 Z= 0.220 Angle : 0.596 15.120 26408 Z= 0.291 Chirality : 0.091 4.356 2908 Planarity : 0.004 0.057 3486 Dihedral : 5.377 92.685 2806 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.07 % Allowed : 15.96 % Favored : 82.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.98 % 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: 0.53 (0.17), residues: 2479 helix: 1.05 (0.16), residues: 1235 sheet: -0.11 (0.50), residues: 119 loop : -0.30 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 447 HIS 0.006 0.001 HIS B 454 PHE 0.025 0.001 PHE X 111 TYR 0.030 0.001 TYR B 102 ARG 0.004 0.000 ARG D 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4829.38 seconds wall clock time: 88 minutes 36.68 seconds (5316.68 seconds total)