Starting phenix.real_space_refine on Mon Apr 8 09:02:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/04_2024/8j5r_35991_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/04_2024/8j5r_35991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/04_2024/8j5r_35991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/04_2024/8j5r_35991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/04_2024/8j5r_35991_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/04_2024/8j5r_35991_updated.pdb" } resolution = 3.28 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= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 42 5.16 5 C 8284 2.51 5 N 2322 2.21 5 O 2398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 76": "OD1" <-> "OD2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ARG 527": "NH1" <-> "NH2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D ASP 446": "OD1" <-> "OD2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "D GLU 499": "OE1" <-> "OE2" Residue "D ASP 524": "OD1" <-> "OD2" Residue "D ASP 531": "OD1" <-> "OD2" Residue "D PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 559": "OD1" <-> "OD2" Residue "D ASP 583": "OD1" <-> "OD2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "D ASP 607": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13050 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3938 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 28, 'TRANS': 490} Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2476 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2063 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain: "D" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4565 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 35, 'TRANS': 573} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10692 SG CYS D 299 26.965 45.541 153.891 1.00 45.63 S ATOM 10592 SG CYS D 286 27.544 48.860 148.613 1.00 40.82 S ATOM 10639 SG CYS D 292 32.360 48.886 153.417 1.00 41.28 S ATOM 10825 SG CYS D 317 26.763 51.504 154.587 1.00 43.60 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER A 195 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER A 195 " occ=0.47 residue: pdb=" N GLY A 509 " occ=0.48 ... (2 atoms not shown) pdb=" O GLY A 509 " occ=0.48 residue: pdb=" N GLU A 510 " occ=0.48 ... (7 atoms not shown) pdb=" OE2 GLU A 510 " occ=0.48 residue: pdb=" N SER A 511 " occ=0.48 ... (4 atoms not shown) pdb=" OG SER A 511 " occ=0.48 Time building chain proxies: 9.59, per 1000 atoms: 0.73 Number of scatterers: 13050 At special positions: 0 Unit cell: (93.184, 105.664, 172.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 42 16.00 O 2398 8.00 N 2322 7.00 C 8284 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: 6.55 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 701 " pdb="FE1 SF4 D 701 " - pdb=" SG CYS D 299 " pdb="FE2 SF4 D 701 " - pdb=" SG CYS D 286 " pdb="FE4 SF4 D 701 " - pdb=" SG CYS D 317 " pdb="FE3 SF4 D 701 " - pdb=" SG CYS D 292 " Number of angles added : 12 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 11 sheets defined 45.1% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.293A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 236 through 239 No H-bonds generated for 'chain 'A' and resid 236 through 239' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.567A pdb=" N ALA A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 445 through 458 removed outlier: 4.484A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 474 removed outlier: 3.660A pdb=" N PHE A 474 " --> pdb=" O GLY A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 534 through 551 removed outlier: 4.341A pdb=" N ALA A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 30 removed outlier: 3.771A pdb=" N ASN B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 62 through 73 Processing helix chain 'B' and resid 88 through 122 removed outlier: 4.220A pdb=" N GLY B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 141 removed outlier: 3.546A pdb=" N THR B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 181 through 219 removed outlier: 5.131A pdb=" N LEU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 3.598A pdb=" N LEU B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.896A pdb=" N ILE B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 4.040A pdb=" N THR B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 272 removed outlier: 3.605A pdb=" N ALA B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 290 through 318 removed outlier: 3.510A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 323 No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'C' and resid 9 through 17 removed outlier: 3.632A pdb=" N ARG C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 37 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 73 through 109 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 140 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 162 through 173 Processing helix chain 'C' and resid 176 through 184 removed outlier: 3.650A pdb=" N MET C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 197 through 225 removed outlier: 4.845A pdb=" N SER C 202 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 246 removed outlier: 3.945A pdb=" N ALA C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 279 removed outlier: 4.546A pdb=" N PHE C 256 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Proline residue: C 257 - end of helix Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 80 through 83 No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'D' and resid 108 through 119 removed outlier: 4.368A pdb=" N HIS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 125 through 139 removed outlier: 3.844A pdb=" N ARG D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.825A pdb=" N ARG D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 187 through 204 Processing helix chain 'D' and resid 215 through 221 Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 401 through 409 removed outlier: 3.793A pdb=" N GLU D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 427 No H-bonds generated for 'chain 'D' and resid 425 through 427' Processing helix chain 'D' and resid 430 through 436 Processing helix chain 'D' and resid 457 through 468 Proline residue: D 464 - end of helix Processing helix chain 'D' and resid 472 through 486 removed outlier: 4.080A pdb=" N HIS D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 494 removed outlier: 4.117A pdb=" N SER D 494 " --> pdb=" O GLY D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 532 through 549 removed outlier: 4.095A pdb=" N GLY D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 566 removed outlier: 3.720A pdb=" N HIS D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 Processing helix chain 'D' and resid 594 through 602 Processing sheet with id= A, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= B, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.958A pdb=" N SER A 143 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 213 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 204 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= D, first strand: chain 'A' and resid 463 through 467 removed outlier: 6.757A pdb=" N ILE A 486 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE A 342 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 344 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER A 554 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 260 through 265 removed outlier: 6.859A pdb=" N VAL A 273 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 29 through 31 Processing sheet with id= G, first strand: chain 'D' and resid 63 through 65 removed outlier: 3.750A pdb=" N ALA D 11 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL D 12 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ARG D 25 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.943A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 208 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET D 39 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE D 210 " --> pdb=" O MET D 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 417 through 420 removed outlier: 6.663A pdb=" N LEU D 384 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG D 351 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU D 382 " --> pdb=" O ARG D 351 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 359 through 361 removed outlier: 4.208A pdb=" N GLY D 372 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 577 through 583 removed outlier: 6.621A pdb=" N VAL D 572 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 570 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR D 553 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE D 392 " --> pdb=" O TYR D 553 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE D 555 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU D 521 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL D 556 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 523 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN D 441 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASP D 524 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D 443 " --> pdb=" O ASP D 524 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1485 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: 4.05 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 5239 1.39 - 1.62: 7978 1.62 - 1.85: 68 1.85 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 13297 Sorted by residual: bond pdb=" C GLN D 111 " pdb=" O GLN D 111 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.19e-02 7.06e+03 4.00e+01 bond pdb=" C LEU D 483 " pdb=" O LEU D 483 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.73e+01 bond pdb=" CA SER A 499 " pdb=" CB SER A 499 " ideal model delta sigma weight residual 1.534 1.458 0.075 1.45e-02 4.76e+03 2.71e+01 bond pdb=" C VAL D 486 " pdb=" O VAL D 486 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.19e-02 7.06e+03 2.64e+01 bond pdb=" N GLU D 525 " pdb=" CA GLU D 525 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.10e-03 1.98e+04 1.87e+01 ... (remaining 13292 not shown) Histogram of bond angle deviations from ideal: 71.27 - 83.89: 12 83.89 - 96.51: 0 96.51 - 109.14: 1134 109.14 - 121.76: 14186 121.76 - 134.38: 2781 Bond angle restraints: 18113 Sorted by residual: angle pdb=" C THR A 291 " pdb=" CA THR A 291 " pdb=" CB THR A 291 " ideal model delta sigma weight residual 109.80 98.66 11.14 1.23e+00 6.61e-01 8.20e+01 angle pdb=" N LEU A 434 " pdb=" CA LEU A 434 " pdb=" C LEU A 434 " ideal model delta sigma weight residual 109.15 99.35 9.80 1.44e+00 4.82e-01 4.63e+01 angle pdb=" N ASN A 246 " pdb=" CA ASN A 246 " pdb=" C ASN A 246 " ideal model delta sigma weight residual 110.97 103.97 7.00 1.09e+00 8.42e-01 4.12e+01 angle pdb=" C THR A 502 " pdb=" CA THR A 502 " pdb=" CB THR A 502 " ideal model delta sigma weight residual 111.36 101.44 9.92 1.63e+00 3.76e-01 3.71e+01 angle pdb=" N THR A 291 " pdb=" CA THR A 291 " pdb=" C THR A 291 " ideal model delta sigma weight residual 110.64 119.54 -8.90 1.48e+00 4.57e-01 3.62e+01 ... (remaining 18108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6959 17.97 - 35.94: 792 35.94 - 53.91: 178 53.91 - 71.88: 15 71.88 - 89.85: 11 Dihedral angle restraints: 7955 sinusoidal: 3051 harmonic: 4904 Sorted by residual: dihedral pdb=" C ARG A 224 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " pdb=" CB ARG A 224 " ideal model delta harmonic sigma weight residual -122.60 -140.36 17.76 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" N ARG A 224 " pdb=" C ARG A 224 " pdb=" CA ARG A 224 " pdb=" CB ARG A 224 " ideal model delta harmonic sigma weight residual 122.80 137.70 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" C GLU A 222 " pdb=" N GLU A 222 " pdb=" CA GLU A 222 " pdb=" CB GLU A 222 " ideal model delta harmonic sigma weight residual -122.60 -137.44 14.84 0 2.50e+00 1.60e-01 3.53e+01 ... (remaining 7952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2084 0.148 - 0.297: 44 0.297 - 0.445: 7 0.445 - 0.594: 4 0.594 - 0.742: 3 Chirality restraints: 2142 Sorted by residual: chirality pdb=" CA ARG A 224 " pdb=" N ARG A 224 " pdb=" C ARG A 224 " pdb=" CB ARG A 224 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA PRO A 302 " pdb=" N PRO A 302 " pdb=" C PRO A 302 " pdb=" CB PRO A 302 " both_signs ideal model delta sigma weight residual False 2.72 2.06 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA GLU A 222 " pdb=" N GLU A 222 " pdb=" C GLU A 222 " pdb=" CB GLU A 222 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.69e+00 ... (remaining 2139 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 296 " 0.023 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ASP A 296 " -0.084 2.00e-02 2.50e+03 pdb=" O ASP A 296 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP A 297 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 466 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C LEU A 466 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 466 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN A 467 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 157 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C THR A 157 " -0.061 2.00e-02 2.50e+03 pdb=" O THR A 157 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 158 " 0.021 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 462 2.70 - 3.25: 13340 3.25 - 3.80: 19653 3.80 - 4.35: 25398 4.35 - 4.90: 44039 Nonbonded interactions: 102892 Sorted by model distance: nonbonded pdb=" O ASN A 407 " pdb=" OD1 ASN A 407 " model vdw 2.145 3.040 nonbonded pdb=" N GLU D 432 " pdb=" OE1 GLU D 432 " model vdw 2.176 2.520 nonbonded pdb=" OD1 ASN A 277 " pdb=" N ARG A 279 " model vdw 2.225 2.520 nonbonded pdb=" O ASP A 266 " pdb=" N ALA A 269 " model vdw 2.227 2.520 nonbonded pdb=" O PHE B 145 " pdb=" ND2 ASN B 149 " model vdw 2.241 2.520 ... (remaining 102887 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=0.47 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 12.270 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 42.600 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 13297 Z= 0.492 Angle : 0.961 11.137 18113 Z= 0.594 Chirality : 0.067 0.742 2142 Planarity : 0.006 0.107 2347 Dihedral : 15.638 89.855 4811 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.22 % Allowed : 1.32 % Favored : 98.46 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 1.16 % 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: -1.53 (0.20), residues: 1718 helix: 0.19 (0.18), residues: 821 sheet: -2.49 (0.37), residues: 179 loop : -2.00 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 280 HIS 0.006 0.001 HIS D 153 PHE 0.024 0.002 PHE A 484 TYR 0.015 0.002 TYR A 406 ARG 0.010 0.001 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.607 Fit side-chains REVERT: D 406 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7936 (tm-30) outliers start: 3 outliers final: 1 residues processed: 140 average time/residue: 0.3123 time to fit residues: 60.9445 Evaluate side-chains 110 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.0370 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 488 GLN C 230 GLN D 81 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13297 Z= 0.198 Angle : 0.596 8.547 18113 Z= 0.306 Chirality : 0.042 0.190 2142 Planarity : 0.005 0.040 2347 Dihedral : 4.746 27.933 1894 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.88 % Allowed : 9.18 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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 (0.21), residues: 1718 helix: 0.62 (0.19), residues: 817 sheet: -2.36 (0.37), residues: 181 loop : -1.67 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 172 HIS 0.005 0.001 HIS D 558 PHE 0.020 0.001 PHE C 109 TYR 0.014 0.001 TYR A 156 ARG 0.007 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.356 Fit side-chains REVERT: A 238 MET cc_start: 0.7042 (tpp) cc_final: 0.6784 (tpp) REVERT: C 230 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8751 (mm110) REVERT: D 406 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7989 (tm-30) outliers start: 12 outliers final: 7 residues processed: 131 average time/residue: 0.2651 time to fit residues: 50.4846 Evaluate side-chains 120 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 0.0030 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 overall best weight: 2.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 230 GLN D 81 ASN D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13297 Z= 0.342 Angle : 0.601 8.094 18113 Z= 0.308 Chirality : 0.043 0.195 2142 Planarity : 0.004 0.040 2347 Dihedral : 4.611 19.370 1890 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.69 % Allowed : 13.00 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.97 (0.21), residues: 1718 helix: 0.66 (0.19), residues: 808 sheet: -2.34 (0.37), residues: 182 loop : -1.67 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 172 HIS 0.004 0.001 HIS A 341 PHE 0.015 0.002 PHE A 484 TYR 0.014 0.002 TYR C 108 ARG 0.006 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.547 Fit side-chains REVERT: A 238 MET cc_start: 0.7116 (tpp) cc_final: 0.6818 (tpp) REVERT: B 169 TYR cc_start: 0.8723 (p90) cc_final: 0.8265 (p90) REVERT: C 204 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8081 (mp) REVERT: D 406 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 23 outliers final: 13 residues processed: 128 average time/residue: 0.2546 time to fit residues: 48.3298 Evaluate side-chains 125 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 212 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13297 Z= 0.329 Angle : 0.583 8.051 18113 Z= 0.298 Chirality : 0.043 0.192 2142 Planarity : 0.004 0.041 2347 Dihedral : 4.547 19.721 1890 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.84 % Allowed : 15.93 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.88 (0.21), residues: 1718 helix: 0.76 (0.19), residues: 799 sheet: -2.28 (0.37), residues: 182 loop : -1.62 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.004 0.001 HIS D 558 PHE 0.015 0.001 PHE C 177 TYR 0.016 0.001 TYR B 66 ARG 0.006 0.000 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.539 Fit side-chains REVERT: A 238 MET cc_start: 0.7228 (tpp) cc_final: 0.6922 (tpp) REVERT: B 169 TYR cc_start: 0.8718 (p90) cc_final: 0.8263 (p90) REVERT: B 280 TRP cc_start: 0.9611 (OUTLIER) cc_final: 0.8715 (t60) REVERT: C 204 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8154 (mp) REVERT: D 406 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8038 (tm-30) outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 0.2552 time to fit residues: 49.3843 Evaluate side-chains 123 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.0050 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 0.0270 chunk 122 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 0.0020 chunk 113 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 433 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13297 Z= 0.130 Angle : 0.509 7.469 18113 Z= 0.258 Chirality : 0.040 0.170 2142 Planarity : 0.004 0.041 2347 Dihedral : 4.101 20.586 1890 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.32 % Allowed : 17.91 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.45 (0.21), residues: 1718 helix: 1.07 (0.19), residues: 805 sheet: -2.06 (0.38), residues: 181 loop : -1.35 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.012 0.001 PHE A 484 TYR 0.017 0.001 TYR B 66 ARG 0.004 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.498 Fit side-chains REVERT: A 238 MET cc_start: 0.7080 (tpp) cc_final: 0.6873 (tpp) REVERT: B 280 TRP cc_start: 0.9550 (OUTLIER) cc_final: 0.8618 (t60) REVERT: C 204 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7983 (mp) outliers start: 18 outliers final: 12 residues processed: 148 average time/residue: 0.2597 time to fit residues: 56.3583 Evaluate side-chains 133 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 356 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13297 Z= 0.170 Angle : 0.507 7.639 18113 Z= 0.257 Chirality : 0.040 0.224 2142 Planarity : 0.004 0.044 2347 Dihedral : 3.985 19.491 1890 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.98 % Allowed : 17.69 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1718 helix: 1.23 (0.19), residues: 795 sheet: -1.94 (0.38), residues: 182 loop : -1.30 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.003 0.001 HIS D 558 PHE 0.015 0.001 PHE A 484 TYR 0.018 0.001 TYR B 66 ARG 0.003 0.000 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 1.466 Fit side-chains REVERT: A 238 MET cc_start: 0.7099 (tpp) cc_final: 0.6874 (tpp) REVERT: B 280 TRP cc_start: 0.9535 (OUTLIER) cc_final: 0.8654 (t60) outliers start: 27 outliers final: 16 residues processed: 142 average time/residue: 0.2662 time to fit residues: 55.0025 Evaluate side-chains 135 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 356 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 433 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13297 Z= 0.279 Angle : 0.535 7.836 18113 Z= 0.272 Chirality : 0.042 0.206 2142 Planarity : 0.004 0.044 2347 Dihedral : 4.074 19.886 1890 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.84 % Allowed : 18.58 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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 (0.21), residues: 1718 helix: 1.15 (0.19), residues: 802 sheet: -1.97 (0.38), residues: 187 loop : -1.36 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.003 0.001 HIS D 213 PHE 0.015 0.001 PHE A 484 TYR 0.019 0.001 TYR B 66 ARG 0.006 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.479 Fit side-chains REVERT: A 238 MET cc_start: 0.7229 (tpp) cc_final: 0.6975 (tpp) REVERT: B 66 TYR cc_start: 0.8942 (t80) cc_final: 0.8690 (t80) REVERT: B 169 TYR cc_start: 0.8693 (p90) cc_final: 0.8260 (p90) REVERT: B 280 TRP cc_start: 0.9568 (OUTLIER) cc_final: 0.8712 (t60) outliers start: 25 outliers final: 17 residues processed: 137 average time/residue: 0.2692 time to fit residues: 53.9525 Evaluate side-chains 134 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 356 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.0370 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 433 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13297 Z= 0.149 Angle : 0.504 7.565 18113 Z= 0.256 Chirality : 0.040 0.203 2142 Planarity : 0.004 0.044 2347 Dihedral : 3.935 20.197 1890 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.98 % Allowed : 18.50 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1718 helix: 1.30 (0.19), residues: 795 sheet: -1.81 (0.39), residues: 182 loop : -1.22 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.003 0.000 HIS D 558 PHE 0.013 0.001 PHE A 484 TYR 0.017 0.001 TYR B 66 ARG 0.006 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.492 Fit side-chains REVERT: A 76 ASP cc_start: 0.8459 (t70) cc_final: 0.8203 (t70) REVERT: A 238 MET cc_start: 0.7149 (tpp) cc_final: 0.6915 (tpp) REVERT: B 66 TYR cc_start: 0.8861 (t80) cc_final: 0.8624 (t80) REVERT: B 280 TRP cc_start: 0.9524 (OUTLIER) cc_final: 0.8637 (t60) outliers start: 27 outliers final: 21 residues processed: 142 average time/residue: 0.2704 time to fit residues: 56.1160 Evaluate side-chains 141 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 0.0870 chunk 100 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13297 Z= 0.151 Angle : 0.501 7.580 18113 Z= 0.254 Chirality : 0.040 0.194 2142 Planarity : 0.004 0.044 2347 Dihedral : 3.862 19.901 1890 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.91 % Allowed : 18.58 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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 (0.21), residues: 1718 helix: 1.38 (0.19), residues: 793 sheet: -1.77 (0.39), residues: 182 loop : -1.16 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.003 0.000 HIS D 558 PHE 0.013 0.001 PHE A 484 TYR 0.016 0.001 TYR B 66 ARG 0.006 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.520 Fit side-chains REVERT: A 76 ASP cc_start: 0.8434 (t70) cc_final: 0.8168 (t70) REVERT: A 238 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6915 (tpp) REVERT: B 66 TYR cc_start: 0.8852 (t80) cc_final: 0.8626 (t80) REVERT: B 280 TRP cc_start: 0.9522 (OUTLIER) cc_final: 0.8631 (t60) outliers start: 26 outliers final: 23 residues processed: 143 average time/residue: 0.2678 time to fit residues: 56.1087 Evaluate side-chains 142 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 14 optimal weight: 0.0060 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 0.0670 chunk 143 optimal weight: 0.7980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13297 Z= 0.137 Angle : 0.495 7.444 18113 Z= 0.250 Chirality : 0.040 0.187 2142 Planarity : 0.004 0.045 2347 Dihedral : 3.772 20.021 1890 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.76 % Allowed : 18.72 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.03 (0.21), residues: 1718 helix: 1.48 (0.19), residues: 791 sheet: -1.72 (0.39), residues: 182 loop : -1.11 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.003 0.000 HIS D 558 PHE 0.012 0.001 PHE A 484 TYR 0.014 0.001 TYR B 66 ARG 0.006 0.000 ARG A 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.361 Fit side-chains REVERT: A 76 ASP cc_start: 0.8383 (t70) cc_final: 0.8123 (t70) REVERT: A 238 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6945 (tpp) REVERT: A 265 LEU cc_start: 0.8979 (pt) cc_final: 0.8672 (pt) REVERT: B 280 TRP cc_start: 0.9506 (OUTLIER) cc_final: 0.8704 (t60) outliers start: 24 outliers final: 21 residues processed: 146 average time/residue: 0.2450 time to fit residues: 52.5181 Evaluate side-chains 143 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 135 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086743 restraints weight = 22861.533| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.26 r_work: 0.2964 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13297 Z= 0.187 Angle : 0.511 7.596 18113 Z= 0.259 Chirality : 0.040 0.190 2142 Planarity : 0.004 0.044 2347 Dihedral : 3.774 19.496 1890 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.98 % Allowed : 18.80 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.03 (0.21), residues: 1718 helix: 1.47 (0.19), residues: 791 sheet: -1.65 (0.39), residues: 182 loop : -1.12 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 339 HIS 0.003 0.001 HIS D 558 PHE 0.013 0.001 PHE A 484 TYR 0.015 0.001 TYR B 66 ARG 0.005 0.000 ARG A 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.98 seconds wall clock time: 53 minutes 45.29 seconds (3225.29 seconds total)