Starting phenix.real_space_refine on Mon Apr 8 10:05:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/04_2024/8j5q_35990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/04_2024/8j5q_35990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/04_2024/8j5q_35990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/04_2024/8j5q_35990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/04_2024/8j5q_35990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/04_2024/8j5q_35990_updated.pdb" } resolution = 3.25 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= 0.008 sd= 0.079 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 41 5.16 5 C 8365 2.51 5 N 2355 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 66": "OD1" <-> "OD2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ARG 527": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "B ARG 3": "NH1" <-> "NH2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D ARG 353": "NH1" <-> "NH2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D ARG 433": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 446": "OD1" <-> "OD2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 474": "OE1" <-> "OE2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "D ASP 492": "OD1" <-> "OD2" Residue "D ARG 495": "NH1" <-> "NH2" Residue "D TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ASP 524": "OD1" <-> "OD2" Residue "D ASP 531": "OD1" <-> "OD2" Residue "D ASP 544": "OD1" <-> "OD2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 597": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 611": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13187 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4003 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 28, 'TRANS': 498} 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: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2070 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 260} Chain: "D" Number of atoms: 4584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4584 Classifications: {'peptide': 611} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 575} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 46 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 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 10656 SG CYS D 286 16.028 52.203 22.637 1.00 72.25 S ATOM 10889 SG CYS D 317 16.301 50.748 16.183 1.00 79.80 S ATOM 10703 SG CYS D 292 19.087 55.724 18.421 1.00 68.73 S ATOM 10756 SG CYS D 299 12.432 55.636 17.637 1.00 87.74 S Time building chain proxies: 7.28, per 1000 atoms: 0.55 Number of scatterers: 13187 At special positions: 0 Unit cell: (80.704, 96.512, 166.4, 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 41 16.00 O 2422 8.00 N 2355 7.00 C 8365 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: 5.30 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D2001 " pdb="FE3 SF4 D2001 " - pdb=" SG CYS D 292 " pdb="FE1 SF4 D2001 " - pdb=" SG CYS D 286 " pdb="FE4 SF4 D2001 " - pdb=" SG CYS D 299 " pdb="FE2 SF4 D2001 " - pdb=" SG CYS D 317 " Number of angles added : 12 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 15 sheets defined 47.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 112 through 120 removed outlier: 5.064A 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 221 through 225 removed outlier: 4.502A pdb=" N ARG A 224 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 239 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.603A pdb=" N LEU A 301 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.638A 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 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.900A pdb=" N GLN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 497 through 504 removed outlier: 4.604A pdb=" N THR A 502 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.952A pdb=" N ALA A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 removed outlier: 3.556A pdb=" N ASN B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 39 removed outlier: 4.127A pdb=" N SER B 36 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 62 through 75 removed outlier: 4.174A pdb=" N ARG B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 122 removed outlier: 4.203A pdb=" N GLY B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 141 Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.702A pdb=" N ASN B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 220 removed outlier: 4.141A pdb=" N ARG B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 3.536A pdb=" N LEU B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.538A pdb=" N ARG B 228 " --> pdb=" O ARG B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 272 removed outlier: 4.443A pdb=" N ARG B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 245 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.813A pdb=" N THR B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TYR B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 286 removed outlier: 3.505A pdb=" N VAL B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 318 removed outlier: 3.573A pdb=" N VAL B 304 " --> pdb=" O SER B 300 " (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 16 Processing helix chain 'C' and resid 19 through 37 removed outlier: 3.906A pdb=" N TYR C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) 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 111 through 126 removed outlier: 3.537A pdb=" N TRP C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.524A pdb=" N VAL C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.755A pdb=" N PHE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 3.726A pdb=" N ARG C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 removed outlier: 3.682A pdb=" N ARG C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 3.553A 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 196 through 224 removed outlier: 4.726A pdb=" N SER C 202 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 4.312A pdb=" N ALA C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 279 Proline residue: C 257 - end of helix Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.533A pdb=" N VAL D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 removed outlier: 4.504A pdb=" N ARG D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.514A pdb=" N ALA D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.443A pdb=" N ARG D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.242A 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 169 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 297 through 300 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 400 through 409 Processing helix chain 'D' and resid 430 through 438 removed outlier: 3.663A pdb=" N SER D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 No H-bonds generated for 'chain 'D' and resid 447 through 450' Processing helix chain 'D' and resid 457 through 467 Proline residue: D 464 - end of helix Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.895A pdb=" N HIS D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 484 " --> pdb=" O ALA D 480 " (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 502 through 516 removed outlier: 5.254A pdb=" N LEU D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 549 removed outlier: 3.785A pdb=" N GLY D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 566 removed outlier: 4.019A 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 601 Processing helix chain 'D' and resid 608 through 610 No H-bonds generated for 'chain 'D' and resid 608 through 610' Processing sheet with id= A, first strand: chain 'A' and resid 90 through 95 removed outlier: 7.039A pdb=" N SER A 289 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LEU A 93 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR A 291 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 95 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 293 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL A 262 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 145 through 148 removed outlier: 6.834A pdb=" N VAL A 153 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 311 through 313 Processing sheet with id= E, first strand: chain 'A' and resid 486 through 491 removed outlier: 3.531A pdb=" N THR A 558 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 342 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 344 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER A 554 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.627A pdb=" N PHE A 426 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 435 through 441 removed outlier: 6.730A pdb=" N LYS A 463 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP A 438 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A 465 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE A 440 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN A 467 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 29 through 31 Processing sheet with id= I, first strand: chain 'D' and resid 62 through 65 removed outlier: 7.453A pdb=" N VAL D 12 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG D 25 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 232 through 238 removed outlier: 6.755A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL D 208 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET D 39 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 210 " --> pdb=" O MET D 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 417 through 420 removed outlier: 6.685A pdb=" N LEU D 384 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG D 351 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU D 382 " --> pdb=" O ARG D 351 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 577 through 583 removed outlier: 6.792A pdb=" N VAL D 572 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 570 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR D 553 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE D 392 " --> pdb=" O TYR D 553 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE D 555 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN D 441 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.827A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 355 through 357 removed outlier: 7.297A pdb=" N LYS D 357 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP D 378 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 359 through 363 removed outlier: 6.460A pdb=" N LYS D 363 " --> pdb=" O ALA D 370 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA D 370 " --> pdb=" O LYS D 363 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1632 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: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 5372 1.41 - 1.63: 7986 1.63 - 1.85: 66 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 13436 Sorted by residual: bond pdb=" C GLU D 525 " pdb=" O GLU D 525 " ideal model delta sigma weight residual 1.234 1.260 -0.026 5.00e-03 4.00e+04 2.68e+01 bond pdb=" N VAL B 177 " pdb=" CA VAL B 177 " ideal model delta sigma weight residual 1.457 1.495 -0.038 9.30e-03 1.16e+04 1.71e+01 bond pdb=" CA SER B 311 " pdb=" CB SER B 311 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.59e-02 3.96e+03 1.54e+01 bond pdb=" C SER B 311 " pdb=" O SER B 311 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.19e-02 7.06e+03 1.45e+01 bond pdb=" N VAL D 164 " pdb=" CA VAL D 164 " ideal model delta sigma weight residual 1.460 1.503 -0.044 1.21e-02 6.83e+03 1.32e+01 ... (remaining 13431 not shown) Histogram of bond angle deviations from ideal: 73.71 - 86.34: 12 86.34 - 98.96: 2 98.96 - 111.58: 6310 111.58 - 124.20: 11612 124.20 - 136.82: 367 Bond angle restraints: 18303 Sorted by residual: angle pdb=" N ALA D 170 " pdb=" CA ALA D 170 " pdb=" C ALA D 170 " ideal model delta sigma weight residual 110.43 103.80 6.63 1.31e+00 5.83e-01 2.56e+01 angle pdb=" CA GLY B 176 " pdb=" C GLY B 176 " pdb=" O GLY B 176 " ideal model delta sigma weight residual 121.88 118.12 3.76 7.80e-01 1.64e+00 2.32e+01 angle pdb=" N VAL B 177 " pdb=" CA VAL B 177 " pdb=" C VAL B 177 " ideal model delta sigma weight residual 113.20 108.68 4.52 9.60e-01 1.09e+00 2.21e+01 angle pdb=" N PHE C 177 " pdb=" CA PHE C 177 " pdb=" C PHE C 177 " ideal model delta sigma weight residual 111.71 106.33 5.38 1.15e+00 7.56e-01 2.19e+01 angle pdb=" N ALA B 307 " pdb=" CA ALA B 307 " pdb=" C ALA B 307 " ideal model delta sigma weight residual 111.28 106.21 5.07 1.09e+00 8.42e-01 2.16e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7125 18.00 - 36.00: 712 36.00 - 53.99: 161 53.99 - 71.99: 32 71.99 - 89.99: 6 Dihedral angle restraints: 8036 sinusoidal: 3077 harmonic: 4959 Sorted by residual: dihedral pdb=" CD ARG D 246 " pdb=" NE ARG D 246 " pdb=" CZ ARG D 246 " pdb=" NH1 ARG D 246 " ideal model delta sinusoidal sigma weight residual 0.00 -51.12 51.12 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA TYR D 553 " pdb=" C TYR D 553 " pdb=" N LEU D 554 " pdb=" CA LEU D 554 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA A 120 " pdb=" C ALA A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta harmonic sigma weight residual 180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 8033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1520 0.053 - 0.106: 498 0.106 - 0.159: 127 0.159 - 0.212: 12 0.212 - 0.265: 4 Chirality restraints: 2161 Sorted by residual: chirality pdb=" CA ARG D 246 " pdb=" N ARG D 246 " pdb=" C ARG D 246 " pdb=" CB ARG D 246 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA SER B 41 " pdb=" N SER B 41 " pdb=" C SER B 41 " pdb=" CB SER B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE C 178 " pdb=" N ILE C 178 " pdb=" C ILE C 178 " pdb=" CB ILE C 178 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2158 not shown) Planarity restraints: 2375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 246 " -0.854 9.50e-02 1.11e+02 3.83e-01 8.89e+01 pdb=" NE ARG D 246 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG D 246 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 246 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 246 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 167 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE D 167 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE D 167 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA D 168 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " -0.261 9.50e-02 1.11e+02 1.17e-01 8.37e+00 pdb=" NE ARG A 92 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2372 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2094 2.75 - 3.29: 13475 3.29 - 3.83: 21027 3.83 - 4.36: 25487 4.36 - 4.90: 43614 Nonbonded interactions: 105697 Sorted by model distance: nonbonded pdb=" OG SER C 45 " pdb=" O TYR C 46 " model vdw 2.216 2.440 nonbonded pdb=" N GLU D 395 " pdb=" OE1 GLU D 395 " model vdw 2.220 2.520 nonbonded pdb=" O VAL D 420 " pdb=" OG1 THR D 423 " model vdw 2.223 2.440 nonbonded pdb=" O HIS A 180 " pdb=" OG SER A 183 " model vdw 2.270 2.440 nonbonded pdb=" O ALA A 303 " pdb=" OG1 THR A 308 " model vdw 2.277 2.440 ... (remaining 105692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.290 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.710 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.008 0.086 13436 Z= 0.558 Angle : 0.930 11.821 18303 Z= 0.554 Chirality : 0.055 0.265 2161 Planarity : 0.010 0.383 2375 Dihedral : 15.303 89.990 4856 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -1.09 (0.19), residues: 1729 helix: -0.39 (0.17), residues: 813 sheet: -0.21 (0.40), residues: 156 loop : -1.09 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 223 HIS 0.007 0.001 HIS A 106 PHE 0.023 0.003 PHE A 474 TYR 0.027 0.004 TYR B 315 ARG 0.011 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.426 Fit side-chains REVERT: A 122 LEU cc_start: 0.9129 (mm) cc_final: 0.8927 (mm) REVERT: A 451 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: B 222 ASP cc_start: 0.7803 (m-30) cc_final: 0.7471 (t0) REVERT: D 174 ASP cc_start: 0.6849 (t70) cc_final: 0.6391 (m-30) outliers start: 4 outliers final: 2 residues processed: 168 average time/residue: 0.2706 time to fit residues: 65.5025 Evaluate side-chains 151 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN A 387 ASN B 54 HIS B 190 GLN B 288 GLN D 468 ASN D 476 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13436 Z= 0.197 Angle : 0.606 8.099 18303 Z= 0.313 Chirality : 0.043 0.166 2161 Planarity : 0.005 0.044 2375 Dihedral : 5.091 54.990 1923 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.17 % Allowed : 7.74 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1729 helix: 0.73 (0.18), residues: 808 sheet: -0.21 (0.38), residues: 168 loop : -0.73 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 223 HIS 0.005 0.001 HIS D 405 PHE 0.016 0.001 PHE A 216 TYR 0.025 0.002 TYR B 4 ARG 0.006 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 180 HIS cc_start: 0.8203 (t70) cc_final: 0.7813 (t70) REVERT: B 222 ASP cc_start: 0.7756 (m-30) cc_final: 0.7457 (t0) REVERT: C 233 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7191 (t0) REVERT: D 247 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6287 (mtm180) REVERT: D 406 GLU cc_start: 0.7679 (tt0) cc_final: 0.7375 (tt0) REVERT: D 590 ASN cc_start: 0.8143 (t0) cc_final: 0.7820 (t0) outliers start: 16 outliers final: 9 residues processed: 177 average time/residue: 0.2835 time to fit residues: 72.2519 Evaluate side-chains 160 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 0.0010 chunk 43 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 overall best weight: 2.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN D 71 GLN D 111 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13436 Z= 0.239 Angle : 0.563 8.001 18303 Z= 0.290 Chirality : 0.042 0.168 2161 Planarity : 0.005 0.042 2375 Dihedral : 4.630 59.018 1918 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.31 % Allowed : 11.61 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.24 (0.20), residues: 1729 helix: 1.08 (0.18), residues: 801 sheet: -0.37 (0.38), residues: 168 loop : -0.65 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.005 0.001 HIS D 558 PHE 0.016 0.001 PHE C 177 TYR 0.024 0.001 TYR B 4 ARG 0.004 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.474 Fit side-chains REVERT: A 148 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7970 (tpp80) REVERT: A 444 GLN cc_start: 0.7332 (tt0) cc_final: 0.7011 (tt0) REVERT: B 222 ASP cc_start: 0.7763 (m-30) cc_final: 0.7536 (t0) REVERT: B 250 MET cc_start: 0.8026 (mmp) cc_final: 0.7449 (mmp) REVERT: C 233 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7314 (t0) REVERT: D 406 GLU cc_start: 0.7654 (tt0) cc_final: 0.7398 (tt0) REVERT: D 590 ASN cc_start: 0.8225 (t0) cc_final: 0.7913 (t0) outliers start: 18 outliers final: 12 residues processed: 168 average time/residue: 0.3022 time to fit residues: 72.1102 Evaluate side-chains 159 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN B 54 HIS B 72 HIS ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13436 Z= 0.228 Angle : 0.534 7.741 18303 Z= 0.274 Chirality : 0.041 0.162 2161 Planarity : 0.004 0.042 2375 Dihedral : 4.468 58.780 1918 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.75 % Allowed : 13.29 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.20), residues: 1729 helix: 1.21 (0.18), residues: 802 sheet: -0.36 (0.39), residues: 167 loop : -0.57 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 280 HIS 0.006 0.001 HIS D 558 PHE 0.012 0.001 PHE C 177 TYR 0.025 0.001 TYR B 4 ARG 0.006 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.785 Fit side-chains REVERT: A 148 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7983 (tpp80) REVERT: A 444 GLN cc_start: 0.7396 (tt0) cc_final: 0.7115 (tt0) REVERT: B 222 ASP cc_start: 0.7750 (m-30) cc_final: 0.7529 (t0) REVERT: B 250 MET cc_start: 0.8074 (mmp) cc_final: 0.7489 (mmp) REVERT: C 122 ASP cc_start: 0.7898 (m-30) cc_final: 0.7624 (m-30) REVERT: C 233 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7349 (t0) REVERT: D 590 ASN cc_start: 0.8267 (t0) cc_final: 0.7962 (t0) outliers start: 24 outliers final: 14 residues processed: 169 average time/residue: 0.2835 time to fit residues: 68.3344 Evaluate side-chains 160 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 123 optimal weight: 0.0000 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 171 ASN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13436 Z= 0.354 Angle : 0.584 7.609 18303 Z= 0.301 Chirality : 0.044 0.174 2161 Planarity : 0.005 0.044 2375 Dihedral : 4.574 59.488 1918 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.97 % Allowed : 14.61 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.20), residues: 1729 helix: 1.02 (0.18), residues: 806 sheet: -0.54 (0.39), residues: 168 loop : -0.60 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 339 HIS 0.006 0.001 HIS D 558 PHE 0.013 0.002 PHE C 177 TYR 0.029 0.002 TYR B 4 ARG 0.004 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.510 Fit side-chains REVERT: B 222 ASP cc_start: 0.7873 (m-30) cc_final: 0.7631 (t0) REVERT: C 14 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8176 (mtp85) REVERT: C 122 ASP cc_start: 0.7899 (m-30) cc_final: 0.7586 (m-30) REVERT: C 233 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7485 (t0) REVERT: D 406 GLU cc_start: 0.7695 (tt0) cc_final: 0.7351 (tt0) REVERT: D 590 ASN cc_start: 0.8318 (t0) cc_final: 0.8028 (t0) outliers start: 27 outliers final: 20 residues processed: 163 average time/residue: 0.2808 time to fit residues: 66.6116 Evaluate side-chains 159 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13436 Z= 0.257 Angle : 0.543 7.704 18303 Z= 0.279 Chirality : 0.042 0.182 2161 Planarity : 0.004 0.044 2375 Dihedral : 4.470 59.736 1918 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.83 % Allowed : 16.14 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1729 helix: 1.13 (0.18), residues: 804 sheet: -0.58 (0.39), residues: 169 loop : -0.56 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.005 0.001 HIS D 558 PHE 0.012 0.001 PHE C 177 TYR 0.025 0.002 TYR B 4 ARG 0.004 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.501 Fit side-chains REVERT: A 444 GLN cc_start: 0.7494 (tt0) cc_final: 0.7221 (tt0) REVERT: B 250 MET cc_start: 0.8022 (mmp) cc_final: 0.7447 (mmp) REVERT: C 122 ASP cc_start: 0.7893 (m-30) cc_final: 0.7614 (m-30) REVERT: C 233 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7383 (t0) REVERT: D 406 GLU cc_start: 0.7660 (tt0) cc_final: 0.7285 (tt0) REVERT: D 590 ASN cc_start: 0.8317 (t0) cc_final: 0.8044 (t0) outliers start: 25 outliers final: 20 residues processed: 167 average time/residue: 0.2789 time to fit residues: 67.2497 Evaluate side-chains 162 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13436 Z= 0.178 Angle : 0.507 7.459 18303 Z= 0.261 Chirality : 0.040 0.176 2161 Planarity : 0.004 0.044 2375 Dihedral : 4.280 59.933 1918 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.68 % Allowed : 16.95 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.20), residues: 1729 helix: 1.37 (0.18), residues: 800 sheet: -0.72 (0.39), residues: 174 loop : -0.42 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.005 0.001 HIS D 558 PHE 0.011 0.001 PHE C 177 TYR 0.021 0.001 TYR B 4 ARG 0.009 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.447 Fit side-chains REVERT: A 444 GLN cc_start: 0.7466 (tt0) cc_final: 0.7240 (tt0) REVERT: B 168 ASP cc_start: 0.8435 (t0) cc_final: 0.8169 (t0) REVERT: C 122 ASP cc_start: 0.7920 (m-30) cc_final: 0.7679 (m-30) REVERT: C 233 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7287 (t0) REVERT: D 122 ARG cc_start: 0.6244 (mtm-85) cc_final: 0.5958 (mtm-85) REVERT: D 590 ASN cc_start: 0.8322 (t0) cc_final: 0.8055 (t0) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 0.2719 time to fit residues: 68.7753 Evaluate side-chains 160 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 150 optimal weight: 0.0970 chunk 158 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13436 Z= 0.265 Angle : 0.538 7.438 18303 Z= 0.277 Chirality : 0.042 0.190 2161 Planarity : 0.004 0.047 2375 Dihedral : 4.320 59.656 1918 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.83 % Allowed : 17.31 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.20), residues: 1729 helix: 1.31 (0.18), residues: 800 sheet: -0.78 (0.39), residues: 174 loop : -0.47 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 280 HIS 0.005 0.001 HIS D 558 PHE 0.011 0.001 PHE C 177 TYR 0.025 0.001 TYR B 4 ARG 0.006 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.419 Fit side-chains REVERT: A 444 GLN cc_start: 0.7523 (tt0) cc_final: 0.7267 (tt0) REVERT: C 122 ASP cc_start: 0.7936 (m-30) cc_final: 0.7655 (m-30) REVERT: C 233 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7333 (t0) REVERT: D 590 ASN cc_start: 0.8362 (t0) cc_final: 0.8108 (t0) outliers start: 25 outliers final: 20 residues processed: 157 average time/residue: 0.2806 time to fit residues: 63.4046 Evaluate side-chains 160 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 139 optimal weight: 0.0670 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13436 Z= 0.283 Angle : 0.554 7.579 18303 Z= 0.285 Chirality : 0.042 0.197 2161 Planarity : 0.004 0.049 2375 Dihedral : 4.388 59.751 1918 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.12 % Allowed : 17.02 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.38 (0.20), residues: 1729 helix: 1.24 (0.18), residues: 806 sheet: -0.89 (0.39), residues: 175 loop : -0.47 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.024 0.001 PHE C 256 TYR 0.026 0.001 TYR B 4 ARG 0.007 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.507 Fit side-chains REVERT: A 444 GLN cc_start: 0.7517 (tt0) cc_final: 0.7300 (tt0) REVERT: C 122 ASP cc_start: 0.7940 (m-30) cc_final: 0.7649 (m-30) REVERT: C 233 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7345 (t0) REVERT: D 122 ARG cc_start: 0.6338 (mtm-85) cc_final: 0.5887 (mtm-85) REVERT: D 590 ASN cc_start: 0.8356 (t0) cc_final: 0.8130 (t0) outliers start: 29 outliers final: 24 residues processed: 159 average time/residue: 0.2822 time to fit residues: 64.8437 Evaluate side-chains 159 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 145 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13436 Z= 0.141 Angle : 0.501 7.205 18303 Z= 0.257 Chirality : 0.040 0.190 2161 Planarity : 0.004 0.049 2375 Dihedral : 4.171 59.523 1918 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.24 % Allowed : 18.04 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.66 (0.20), residues: 1729 helix: 1.54 (0.19), residues: 799 sheet: -0.82 (0.39), residues: 174 loop : -0.38 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 280 HIS 0.004 0.001 HIS B 275 PHE 0.016 0.001 PHE C 256 TYR 0.018 0.001 TYR B 4 ARG 0.007 0.000 ARG A 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.458 Fit side-chains REVERT: A 444 GLN cc_start: 0.7454 (tt0) cc_final: 0.7241 (tt0) REVERT: B 168 ASP cc_start: 0.8396 (t0) cc_final: 0.8137 (t0) REVERT: C 122 ASP cc_start: 0.7912 (m-30) cc_final: 0.7687 (m-30) REVERT: C 233 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7234 (t0) REVERT: D 122 ARG cc_start: 0.6276 (mtm-85) cc_final: 0.5853 (mtm-85) outliers start: 17 outliers final: 13 residues processed: 158 average time/residue: 0.2762 time to fit residues: 63.4356 Evaluate side-chains 156 residues out of total 1369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101255 restraints weight = 19410.784| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.07 r_work: 0.3049 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13436 Z= 0.231 Angle : 0.530 6.934 18303 Z= 0.272 Chirality : 0.041 0.196 2161 Planarity : 0.004 0.047 2375 Dihedral : 4.223 59.958 1918 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.24 % Allowed : 18.26 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.60 (0.20), residues: 1729 helix: 1.50 (0.18), residues: 799 sheet: -0.84 (0.39), residues: 174 loop : -0.42 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.017 0.001 PHE C 256 TYR 0.023 0.001 TYR B 4 ARG 0.007 0.000 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.69 seconds wall clock time: 53 minutes 20.54 seconds (3200.54 seconds total)