Starting phenix.real_space_refine (version: dev) on Tue Dec 20 10:53:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mop_23925/12_2022/7mop_23925.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mop_23925/12_2022/7mop_23925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mop_23925/12_2022/7mop_23925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mop_23925/12_2022/7mop_23925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mop_23925/12_2022/7mop_23925.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mop_23925/12_2022/7mop_23925.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 24": "OD1" <-> "OD2" Residue "A ASP 31": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ARG 364": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A ARG 616": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 645": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A ASP 676": "OD1" <-> "OD2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A ASP 768": "OD1" <-> "OD2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A GLU 965": "OE1" <-> "OE2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1125": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1193": "OD1" <-> "OD2" Residue "A GLU 1197": "OE1" <-> "OE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A PHE 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1284": "OE1" <-> "OE2" Residue "A GLU 1294": "OE1" <-> "OE2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A ASP 1427": "OD1" <-> "OD2" Residue "A GLU 1432": "OE1" <-> "OE2" Residue "A ASP 1434": "OD1" <-> "OD2" Residue "A PHE 1439": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1452": "OD1" <-> "OD2" Residue "A ASP 1456": "OD1" <-> "OD2" Residue "A ASP 1463": "OD1" <-> "OD2" Residue "A ARG 1471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 1478": "OD1" <-> "OD2" Residue "A GLU 1490": "OE1" <-> "OE2" Residue "A GLU 1512": "OE1" <-> "OE2" Residue "A GLU 1539": "OE1" <-> "OE2" Residue "A GLU 1549": "OE1" <-> "OE2" Residue "A GLU 1573": "OE1" <-> "OE2" Residue "A GLU 1576": "OE1" <-> "OE2" Residue "A TYR 1593": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1603": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1620": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1621": "OD1" <-> "OD2" Residue "A ASP 1622": "OD1" <-> "OD2" Residue "A PHE 1651": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1671": "OE1" <-> "OE2" Residue "A ARG 1675": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1780": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1787": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1816": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1825": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1866": "OE1" <-> "OE2" Residue "A TYR 1869": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1880": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1885": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1909": "OD1" <-> "OD2" Residue "A PHE 1911": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1940": "OD1" <-> "OD2" Residue "A ASP 1948": "OD1" <-> "OD2" Residue "A TYR 2092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2104": "OE1" <-> "OE2" Residue "A ASP 2105": "OD1" <-> "OD2" Residue "A ASP 2114": "OD1" <-> "OD2" Residue "A ASP 2125": "OD1" <-> "OD2" Residue "A ASP 2147": "OD1" <-> "OD2" Residue "A GLU 2168": "OE1" <-> "OE2" Residue "A ASP 2224": "OD1" <-> "OD2" Residue "A GLU 2251": "OE1" <-> "OE2" Residue "A GLU 2653": "OE1" <-> "OE2" Residue "A GLU 2679": "OE1" <-> "OE2" Residue "A ARG 2682": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 2684": "OE1" <-> "OE2" Residue "A GLU 2685": "OE1" <-> "OE2" Residue "A GLU 2688": "OE1" <-> "OE2" Residue "A GLU 2691": "OE1" <-> "OE2" Residue "A ARG 2693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 3196": "OD1" <-> "OD2" Residue "A GLU 3197": "OE1" <-> "OE2" Residue "A ARG 3210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 3219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 3232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 3291": "OD1" <-> "OD2" Residue "A ASP 3387": "OD1" <-> "OD2" Residue "A PHE 3388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 3390": "OD1" <-> "OD2" Residue "A GLU 3427": "OE1" <-> "OE2" Residue "A ARG 3444": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 3451": "OE1" <-> "OE2" Residue "A GLU 3586": "OE1" <-> "OE2" Residue "A GLU 3595": "OE1" <-> "OE2" Residue "A ASP 3600": "OD1" <-> "OD2" Residue "A ASP 3617": "OD1" <-> "OD2" Residue "A GLU 3644": "OE1" <-> "OE2" Residue "A TYR 3648": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 3720": "OE1" <-> "OE2" Residue "A ARG 3750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 3751": "OD1" <-> "OD2" Residue "A ASP 3858": "OD1" <-> "OD2" Residue "A GLU 3868": "OE1" <-> "OE2" Residue "A GLU 3869": "OE1" <-> "OE2" Residue "A GLU 3884": "OE1" <-> "OE2" Residue "A PHE 3886": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 3893": "OE1" <-> "OE2" Residue "A ASP 3979": "OD1" <-> "OD2" Residue "A ASP 4024": "OD1" <-> "OD2" Residue "A TYR 4047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 4054": "OE1" <-> "OE2" Residue "A ASP 4057": "OD1" <-> "OD2" Residue "A GLU 4064": "OE1" <-> "OE2" Residue "A GLU 4072": "OE1" <-> "OE2" Residue "A ASP 4087": "OD1" <-> "OD2" Residue "A TYR 4091": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 4107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 4125": "OE1" <-> "OE2" Residue "A GLU 4147": "OE1" <-> "OE2" Residue "A GLU 4149": "OE1" <-> "OE2" Residue "A TYR 4159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 4177": "OE1" <-> "OE2" Residue "A GLU 4185": "OE1" <-> "OE2" Residue "A ASP 4188": "OD1" <-> "OD2" Residue "A GLU 4205": "OE1" <-> "OE2" Residue "A TYR 4206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 4230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 4246": "OE1" <-> "OE2" Residue "A GLU 4248": "OE1" <-> "OE2" Residue "A ASP 4261": "OD1" <-> "OD2" Residue "A ASP 4289": "OD1" <-> "OD2" Residue "A GLU 4315": "OE1" <-> "OE2" Residue "A ASP 4329": "OD1" <-> "OD2" Residue "A ASP 4346": "OD1" <-> "OD2" Residue "B ASP 6": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 39049 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 38929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2445, 38929 Classifications: {'peptide': 2445} Link IDs: {'PTRANS': 104, 'TRANS': 2340} Chain breaks: 30 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 18.91, per 1000 atoms: 0.48 Number of scatterers: 39049 At special positions: 0 Unit cell: (135.3, 124.575, 169.95, 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) S 122 16.00 O 3566 8.00 N 3325 7.00 C 12355 6.00 H 19681 1.00 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: 35.31 Conformation dependent library (CDL) restraints added in 3.9 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4692 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 10 sheets defined 74.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.824A pdb=" N LEU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 127 through 145 removed outlier: 3.596A pdb=" N VAL A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.787A pdb=" N MET A 188 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 189' Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.202A pdb=" N LEU A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 290 Processing helix chain 'A' and resid 302 through 314 removed outlier: 4.213A pdb=" N ILE A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 379 through 395 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 407 through 419 removed outlier: 4.154A pdb=" N ALA A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 441 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 451 through 471 removed outlier: 3.754A pdb=" N LYS A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.518A pdb=" N SER A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 569 Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 597 through 612 Proline residue: A 605 - end of helix Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.752A pdb=" N CYS A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 removed outlier: 3.717A pdb=" N ARG A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.533A pdb=" N SER A 636 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Proline residue: A 637 - end of helix Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 653 through 670 Processing helix chain 'A' and resid 673 through 694 Processing helix chain 'A' and resid 765 through 782 Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.746A pdb=" N ILE A 805 " --> pdb=" O PRO A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 818 through 836 Processing helix chain 'A' and resid 838 through 853 Processing helix chain 'A' and resid 854 through 859 Proline residue: A 857 - end of helix No H-bonds generated for 'chain 'A' and resid 854 through 859' Processing helix chain 'A' and resid 868 through 876 removed outlier: 3.633A pdb=" N CYS A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.555A pdb=" N LEU A 885 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 911 removed outlier: 3.529A pdb=" N MET A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 908 " --> pdb=" O MET A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 926 Processing helix chain 'A' and resid 927 through 956 Processing helix chain 'A' and resid 967 through 975 removed outlier: 3.746A pdb=" N LYS A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1076 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1097 through 1115 Processing helix chain 'A' and resid 1124 through 1143 removed outlier: 3.525A pdb=" N SER A1139 " --> pdb=" O VAL A1135 " (cutoff:3.500A) Proline residue: A1140 - end of helix Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1162 through 1176 Processing helix chain 'A' and resid 1181 through 1186 removed outlier: 4.131A pdb=" N LEU A1186 " --> pdb=" O VAL A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1211 removed outlier: 3.588A pdb=" N LYS A1208 " --> pdb=" O MET A1204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1237 through 1255 removed outlier: 3.789A pdb=" N THR A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1294 Proline residue: A1285 - end of helix Processing helix chain 'A' and resid 1417 through 1427 Processing helix chain 'A' and resid 1432 through 1443 removed outlier: 3.722A pdb=" N LEU A1436 " --> pdb=" O GLU A1432 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1438 " --> pdb=" O ASP A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1457 through 1472 removed outlier: 3.567A pdb=" N ASP A1463 " --> pdb=" O TYR A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1498 removed outlier: 3.640A pdb=" N MET A1479 " --> pdb=" O ASP A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1520 removed outlier: 3.570A pdb=" N ILE A1514 " --> pdb=" O VAL A1510 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A1518 " --> pdb=" O ILE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1540 removed outlier: 4.103A pdb=" N ALA A1527 " --> pdb=" O ALA A1523 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A1531 " --> pdb=" O ALA A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1551 Processing helix chain 'A' and resid 1552 through 1575 removed outlier: 3.551A pdb=" N GLN A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Proline residue: A1566 - end of helix Processing helix chain 'A' and resid 1582 through 1608 Processing helix chain 'A' and resid 1631 through 1644 Processing helix chain 'A' and resid 1751 through 1768 Processing helix chain 'A' and resid 1771 through 1786 Processing helix chain 'A' and resid 1788 through 1798 Processing helix chain 'A' and resid 1799 through 1807 removed outlier: 3.877A pdb=" N MET A1803 " --> pdb=" O LYS A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1812 removed outlier: 3.557A pdb=" N GLY A1812 " --> pdb=" O GLN A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1829 Processing helix chain 'A' and resid 1830 through 1848 Processing helix chain 'A' and resid 1862 through 1865 Processing helix chain 'A' and resid 1866 through 1874 removed outlier: 3.850A pdb=" N ARG A1872 " --> pdb=" O ASN A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 1874 through 1881 Processing helix chain 'A' and resid 1881 through 1892 Processing helix chain 'A' and resid 1907 through 1917 Processing helix chain 'A' and resid 1939 through 1953 removed outlier: 3.806A pdb=" N ASP A1948 " --> pdb=" O GLU A1944 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A1949 " --> pdb=" O VAL A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2082 Processing helix chain 'A' and resid 2082 through 2092 removed outlier: 3.838A pdb=" N ALA A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2127 through 2142 Processing helix chain 'A' and resid 2148 through 2166 Processing helix chain 'A' and resid 2169 through 2188 Processing helix chain 'A' and resid 2211 through 2219 Processing helix chain 'A' and resid 2220 through 2227 Processing helix chain 'A' and resid 2228 through 2232 Processing helix chain 'A' and resid 2238 through 2259 removed outlier: 3.721A pdb=" N THR A2242 " --> pdb=" O ASN A2238 " (cutoff:3.500A) Proline residue: A2249 - end of helix Processing helix chain 'A' and resid 2646 through 2659 Processing helix chain 'A' and resid 2662 through 2696 removed outlier: 3.819A pdb=" N HIS A2677 " --> pdb=" O SER A2673 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE A2680 " --> pdb=" O ASN A2676 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3195 Processing helix chain 'A' and resid 3201 through 3213 Processing helix chain 'A' and resid 3215 through 3234 Processing helix chain 'A' and resid 3328 through 3346 Processing helix chain 'A' and resid 3388 through 3398 removed outlier: 3.733A pdb=" N MET A3398 " --> pdb=" O LYS A3394 " (cutoff:3.500A) Processing helix chain 'A' and resid 3430 through 3437 Processing helix chain 'A' and resid 3440 through 3446 removed outlier: 3.732A pdb=" N SER A3446 " --> pdb=" O VAL A3442 " (cutoff:3.500A) Processing helix chain 'A' and resid 3446 through 3462 removed outlier: 3.612A pdb=" N ILE A3462 " --> pdb=" O SER A3458 " (cutoff:3.500A) Processing helix chain 'A' and resid 3576 through 3589 removed outlier: 3.559A pdb=" N GLU A3586 " --> pdb=" O GLN A3582 " (cutoff:3.500A) Processing helix chain 'A' and resid 3595 through 3612 Processing helix chain 'A' and resid 3612 through 3650 removed outlier: 4.363A pdb=" N THR A3640 " --> pdb=" O LYS A3636 " (cutoff:3.500A) Processing helix chain 'A' and resid 3723 through 3725 No H-bonds generated for 'chain 'A' and resid 3723 through 3725' Processing helix chain 'A' and resid 3726 through 3731 Processing helix chain 'A' and resid 3734 through 3751 removed outlier: 3.684A pdb=" N ASP A3751 " --> pdb=" O ILE A3747 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3870 Processing helix chain 'A' and resid 3873 through 3878 removed outlier: 4.053A pdb=" N VAL A3878 " --> pdb=" O ALA A3875 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3890 Processing helix chain 'A' and resid 3954 through 3962 Processing helix chain 'A' and resid 3962 through 3973 Processing helix chain 'A' and resid 3980 through 3987 removed outlier: 3.505A pdb=" N ALA A3983 " --> pdb=" O GLY A3980 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A3984 " --> pdb=" O PRO A3981 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A3985 " --> pdb=" O PHE A3982 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A3987 " --> pdb=" O VAL A3984 " (cutoff:3.500A) Processing helix chain 'A' and resid 3988 through 3992 removed outlier: 3.827A pdb=" N VAL A3991 " --> pdb=" O TYR A3988 " (cutoff:3.500A) Processing helix chain 'A' and resid 3993 through 4002 Processing helix chain 'A' and resid 4025 through 4035 Processing helix chain 'A' and resid 4038 through 4043 Processing helix chain 'A' and resid 4057 through 4073 Processing helix chain 'A' and resid 4074 through 4079 removed outlier: 6.174A pdb=" N MET A4077 " --> pdb=" O PHE A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4096 through 4100 removed outlier: 3.802A pdb=" N CYS A4099 " --> pdb=" O SER A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4102 through 4121 Processing helix chain 'A' and resid 4129 through 4138 Processing helix chain 'A' and resid 4144 through 4150 removed outlier: 4.148A pdb=" N SER A4148 " --> pdb=" O THR A4144 " (cutoff:3.500A) Processing helix chain 'A' and resid 4150 through 4161 Processing helix chain 'A' and resid 4164 through 4168 Processing helix chain 'A' and resid 4202 through 4217 removed outlier: 3.692A pdb=" N HIS A4208 " --> pdb=" O LYS A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4219 through 4232 Processing helix chain 'A' and resid 4235 through 4240 Processing helix chain 'A' and resid 4243 through 4252 removed outlier: 3.837A pdb=" N GLU A4248 " --> pdb=" O GLU A4244 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4265 Processing helix chain 'A' and resid 4275 through 4288 Processing helix chain 'A' and resid 4289 through 4302 Processing helix chain 'A' and resid 4310 through 4313 Processing helix chain 'A' and resid 4340 through 4342 No H-bonds generated for 'chain 'A' and resid 4340 through 4342' Processing helix chain 'A' and resid 4352 through 4364 Processing sheet with id=AA1, first strand: chain 'A' and resid 698 through 699 removed outlier: 5.966A pdb=" N ILE A 698 " --> pdb=" O ILE A 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1626 through 1629 Processing sheet with id=AA3, first strand: chain 'A' and resid 1893 through 1895 Processing sheet with id=AA4, first strand: chain 'A' and resid 3289 through 3290 Processing sheet with id=AA5, first strand: chain 'A' and resid 3301 through 3302 Processing sheet with id=AA6, first strand: chain 'A' and resid 4016 through 4021 removed outlier: 5.947A pdb=" N MET A4017 " --> pdb=" O TYR A4047 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A4049 " --> pdb=" O MET A4017 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A4019 " --> pdb=" O VAL A4049 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 4081 through 4082 Processing sheet with id=AA8, first strand: chain 'A' and resid 4175 through 4180 Processing sheet with id=AA9, first strand: chain 'A' and resid 4266 through 4268 removed outlier: 6.810A pdb=" N GLU A4267 " --> pdb=" O ILE A4325 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG A4327 " --> pdb=" O GLU A4267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 4315 through 4316 removed outlier: 3.740A pdb=" N GLY A4319 " --> pdb=" O GLY A4316 " (cutoff:3.500A) 1242 hydrogen bonds defined for protein. 3645 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: 17.26 Time building geometry restraints manager: 36.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 19628 1.00 - 1.20: 53 1.20 - 1.41: 7748 1.41 - 1.61: 11776 1.61 - 1.81: 191 Bond restraints: 39396 Sorted by residual: bond pdb=" NE2 GLN A 275 " pdb="HE22 GLN A 275 " ideal model delta sigma weight residual 0.860 0.799 0.061 2.00e-02 2.50e+03 9.35e+00 bond pdb=" NE2 GLN A 278 " pdb="HE22 GLN A 278 " ideal model delta sigma weight residual 0.860 0.805 0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" N PRO A1140 " pdb=" CD PRO A1140 " ideal model delta sigma weight residual 1.473 1.441 0.032 1.40e-02 5.10e+03 5.38e+00 bond pdb=" CG LEU A 186 " pdb=" CD2 LEU A 186 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CA ALA A1597 " pdb=" C ALA A1597 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.29e-02 6.01e+03 1.88e+00 ... (remaining 39391 not shown) Histogram of bond angle deviations from ideal: 93.69 - 104.26: 326 104.26 - 114.83: 50419 114.83 - 125.40: 19755 125.40 - 135.97: 897 135.97 - 146.54: 2 Bond angle restraints: 71399 Sorted by residual: angle pdb=" CD GLN A 278 " pdb=" NE2 GLN A 278 " pdb="HE22 GLN A 278 " ideal model delta sigma weight residual 120.00 146.54 -26.54 3.00e+00 1.11e-01 7.83e+01 angle pdb="HE21 GLN A 278 " pdb=" NE2 GLN A 278 " pdb="HE22 GLN A 278 " ideal model delta sigma weight residual 120.00 93.69 26.31 3.00e+00 1.11e-01 7.69e+01 angle pdb=" CD GLN A 278 " pdb=" NE2 GLN A 278 " pdb="HE21 GLN A 278 " ideal model delta sigma weight residual 120.00 98.57 21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb="HE21 GLN A 275 " pdb=" NE2 GLN A 275 " pdb="HE22 GLN A 275 " ideal model delta sigma weight residual 120.00 99.21 20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" CD GLN A 275 " pdb=" NE2 GLN A 275 " pdb="HE22 GLN A 275 " ideal model delta sigma weight residual 120.00 140.53 -20.53 3.00e+00 1.11e-01 4.68e+01 ... (remaining 71394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14320 17.98 - 35.96: 1069 35.96 - 53.95: 296 53.95 - 71.93: 70 71.93 - 89.91: 23 Dihedral angle restraints: 15778 sinusoidal: 7586 harmonic: 8192 Sorted by residual: dihedral pdb=" CA GLU A2124 " pdb=" C GLU A2124 " pdb=" N ASP A2125 " pdb=" CA ASP A2125 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TRP A 54 " pdb=" C TRP A 54 " pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ASP A1144 " pdb=" C ASP A1144 " pdb=" N GLU A1145 " pdb=" CA GLU A1145 " ideal model delta harmonic sigma weight residual 180.00 155.47 24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 15775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2820 0.073 - 0.145: 320 0.145 - 0.218: 12 0.218 - 0.291: 1 0.291 - 0.363: 1 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CA ARG A 144 " pdb=" N ARG A 144 " pdb=" C ARG A 144 " pdb=" CB ARG A 144 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE A2513 " pdb=" CA ILE A2513 " pdb=" CG1 ILE A2513 " pdb=" CG2 ILE A2513 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA THR A 157 " pdb=" N THR A 157 " pdb=" C THR A 157 " pdb=" CB THR A 157 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3151 not shown) Planarity restraints: 5677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 275 " -0.059 2.00e-02 2.50e+03 9.56e-02 1.37e+02 pdb=" CD GLN A 275 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 275 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 275 " 0.162 2.00e-02 2.50e+03 pdb="HE21 GLN A 275 " 0.033 2.00e-02 2.50e+03 pdb="HE22 GLN A 275 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 278 " 0.044 2.00e-02 2.50e+03 9.01e-02 1.22e+02 pdb=" CD GLN A 278 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN A 278 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 GLN A 278 " -0.155 2.00e-02 2.50e+03 pdb="HE21 GLN A 278 " -0.042 2.00e-02 2.50e+03 pdb="HE22 GLN A 278 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A4200 " -0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" CD GLU A4200 " 0.088 2.00e-02 2.50e+03 pdb=" OE1 GLU A4200 " -0.032 2.00e-02 2.50e+03 pdb=" OE2 GLU A4200 " -0.031 2.00e-02 2.50e+03 ... (remaining 5674 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 445 2.02 - 2.67: 58296 2.67 - 3.31: 118823 3.31 - 3.96: 148162 3.96 - 4.60: 238143 Nonbonded interactions: 563869 Sorted by model distance: nonbonded pdb=" OD1 ASN A3967 " pdb=" H ASP A3993 " model vdw 1.377 1.850 nonbonded pdb=" O GLU A 181 " pdb=" HH TYR A 191 " model vdw 1.547 1.850 nonbonded pdb=" OE1 GLN A 368 " pdb=" HZ3 LYS A 414 " model vdw 1.556 1.850 nonbonded pdb=" O ARG A4334 " pdb=" HH TYR A4350 " model vdw 1.557 1.850 nonbonded pdb="HH11 ARG A4082 " pdb=" OD1 ASN A4094 " model vdw 1.567 1.850 ... (remaining 563864 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 122 5.16 5 C 12355 2.51 5 N 3325 2.21 5 O 3566 1.98 5 H 19681 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.700 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: 0.570 Extract box with map and model: 13.170 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.310 Process input model: 129.890 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 19715 Z= 0.372 Angle : 0.795 11.667 26687 Z= 0.459 Chirality : 0.045 0.363 3154 Planarity : 0.007 0.051 3361 Dihedral : 14.721 89.911 7336 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2388 helix: -0.21 (0.12), residues: 1667 sheet: 0.63 (0.61), residues: 71 loop : -0.75 (0.24), residues: 650 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 398 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 422 average time/residue: 0.7993 time to fit residues: 502.0323 Evaluate side-chains 228 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 2.944 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4242 time to fit residues: 13.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 278 GLN A 791 GLN A 923 ASN A 924 GLN ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4044 ASN A4358 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19715 Z= 0.219 Angle : 0.594 6.191 26687 Z= 0.309 Chirality : 0.036 0.164 3154 Planarity : 0.005 0.050 3361 Dihedral : 4.617 24.043 2618 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2388 helix: 0.97 (0.12), residues: 1679 sheet: 0.66 (0.56), residues: 71 loop : -0.22 (0.25), residues: 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 242 average time/residue: 0.7274 time to fit residues: 273.1961 Evaluate side-chains 206 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 3.399 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4708 time to fit residues: 17.9655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 197 optimal weight: 0.0670 chunk 220 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 GLN A1613 ASN ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 19715 Z= 0.352 Angle : 0.616 6.791 26687 Z= 0.323 Chirality : 0.039 0.142 3154 Planarity : 0.005 0.048 3361 Dihedral : 4.489 22.986 2618 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2388 helix: 1.17 (0.12), residues: 1690 sheet: 0.41 (0.56), residues: 73 loop : -0.21 (0.26), residues: 625 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 205 average time/residue: 0.7538 time to fit residues: 238.0987 Evaluate side-chains 181 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 3.261 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4113 time to fit residues: 10.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19715 Z= 0.195 Angle : 0.526 6.248 26687 Z= 0.269 Chirality : 0.035 0.135 3154 Planarity : 0.004 0.052 3361 Dihedral : 4.187 20.563 2618 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2388 helix: 1.68 (0.13), residues: 1682 sheet: 0.27 (0.56), residues: 75 loop : -0.11 (0.26), residues: 631 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 196 average time/residue: 0.7234 time to fit residues: 221.3386 Evaluate side-chains 172 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4682 time to fit residues: 10.9090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN A 614 ASN ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 19715 Z= 0.315 Angle : 0.576 6.341 26687 Z= 0.299 Chirality : 0.038 0.143 3154 Planarity : 0.004 0.054 3361 Dihedral : 4.259 20.449 2618 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.17), residues: 2388 helix: 1.59 (0.12), residues: 1684 sheet: 0.09 (0.57), residues: 75 loop : -0.26 (0.26), residues: 629 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 192 average time/residue: 0.7595 time to fit residues: 224.9013 Evaluate side-chains 167 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4790 time to fit residues: 11.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19715 Z= 0.192 Angle : 0.513 5.897 26687 Z= 0.262 Chirality : 0.035 0.135 3154 Planarity : 0.004 0.053 3361 Dihedral : 4.066 19.281 2618 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2388 helix: 1.88 (0.13), residues: 1687 sheet: 0.17 (0.57), residues: 75 loop : -0.20 (0.26), residues: 626 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 184 average time/residue: 0.7267 time to fit residues: 210.1235 Evaluate side-chains 171 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 3.247 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4448 time to fit residues: 11.7213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 147 optimal weight: 0.2980 chunk 143 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 19715 Z= 0.158 Angle : 0.492 5.751 26687 Z= 0.250 Chirality : 0.034 0.136 3154 Planarity : 0.004 0.052 3361 Dihedral : 3.881 17.717 2618 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.18), residues: 2388 helix: 2.15 (0.13), residues: 1687 sheet: 0.29 (0.58), residues: 75 loop : -0.14 (0.26), residues: 626 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 174 average time/residue: 0.7396 time to fit residues: 204.0445 Evaluate side-chains 163 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4237 time to fit residues: 5.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 149 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 19715 Z= 0.140 Angle : 0.476 6.207 26687 Z= 0.241 Chirality : 0.034 0.136 3154 Planarity : 0.004 0.051 3361 Dihedral : 3.736 16.634 2618 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.18), residues: 2388 helix: 2.35 (0.13), residues: 1693 sheet: 0.26 (0.56), residues: 80 loop : -0.09 (0.26), residues: 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 175 average time/residue: 0.6939 time to fit residues: 193.2475 Evaluate side-chains 168 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6621 time to fit residues: 7.2852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 19715 Z= 0.311 Angle : 0.551 5.801 26687 Z= 0.285 Chirality : 0.037 0.152 3154 Planarity : 0.004 0.051 3361 Dihedral : 3.957 17.507 2618 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2388 helix: 2.01 (0.12), residues: 1696 sheet: 0.20 (0.59), residues: 75 loop : -0.29 (0.26), residues: 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 166 average time/residue: 0.7099 time to fit residues: 188.0824 Evaluate side-chains 160 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 3.574 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4289 time to fit residues: 5.1958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19715 Z= 0.185 Angle : 0.497 6.707 26687 Z= 0.253 Chirality : 0.035 0.151 3154 Planarity : 0.004 0.051 3361 Dihedral : 3.846 17.256 2618 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.18), residues: 2388 helix: 2.18 (0.13), residues: 1695 sheet: 0.21 (0.57), residues: 80 loop : -0.22 (0.26), residues: 613 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 3997 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 169 average time/residue: 0.7165 time to fit residues: 193.4216 Evaluate side-chains 161 residues out of total 2173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 3.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 178 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.158002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123712 restraints weight = 90304.448| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.20 r_work: 0.3389 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19715 Z= 0.178 Angle : 0.490 6.453 26687 Z= 0.250 Chirality : 0.035 0.135 3154 Planarity : 0.004 0.050 3361 Dihedral : 3.782 16.741 2618 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.17), residues: 2388 helix: 2.28 (0.13), residues: 1689 sheet: 0.24 (0.57), residues: 80 loop : -0.18 (0.26), residues: 619 =============================================================================== Job complete usr+sys time: 7617.98 seconds wall clock time: 137 minutes 0.08 seconds (8220.08 seconds total)