Starting phenix.real_space_refine on Thu Mar 21 03:35:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4k_17410/03_2024/8p4k_17410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4k_17410/03_2024/8p4k_17410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4k_17410/03_2024/8p4k_17410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4k_17410/03_2024/8p4k_17410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4k_17410/03_2024/8p4k_17410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4k_17410/03_2024/8p4k_17410.pdb" } resolution = 3.8 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= 0.000 sd= 0.205 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 S 78 5.16 5 C 9369 2.51 5 N 2409 2.21 5 O 2712 1.98 5 H 14643 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 575": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29211 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 9737 Classifications: {'peptide': 599} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 573} Chain: "B" Number of atoms: 9737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 9737 Classifications: {'peptide': 599} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 573} Chain: "C" Number of atoms: 9737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 9737 Classifications: {'peptide': 599} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 573} Time building chain proxies: 13.22, per 1000 atoms: 0.45 Number of scatterers: 29211 At special positions: 0 Unit cell: (107.06, 104.94, 118.72, 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 78 16.00 O 2712 8.00 N 2409 7.00 C 9369 6.00 H 14643 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 569 " distance=2.10 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 569 " distance=2.10 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 569 " distance=2.10 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: 23.92 Conformation dependent library (CDL) restraints added in 3.2 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 21 sheets defined 50.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 15 through 18 Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.532A pdb=" N VAL A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 37 through 42 removed outlier: 4.648A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 61 through 82 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 179 Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.832A pdb=" N ASN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.320A pdb=" N VAL A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.544A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 470 through 481 removed outlier: 3.951A pdb=" N MET A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.599A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 removed outlier: 4.649A pdb=" N GLN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 581 through 591 removed outlier: 4.964A pdb=" N PHE A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 15 through 18 Processing helix chain 'B' and resid 19 through 27 removed outlier: 3.532A pdb=" N VAL B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.649A pdb=" N THR B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 53 through 60 Processing helix chain 'B' and resid 61 through 82 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.832A pdb=" N ASN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 218 through 227 Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.320A pdb=" N VAL B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 362 Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.544A pdb=" N LYS B 384 " --> pdb=" O GLU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 470 through 481 removed outlier: 3.951A pdb=" N MET B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.599A pdb=" N LYS B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 529 removed outlier: 4.647A pdb=" N GLN B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'B' and resid 581 through 591 removed outlier: 4.963A pdb=" N PHE B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 15 through 18 Processing helix chain 'C' and resid 19 through 27 removed outlier: 3.532A pdb=" N VAL C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 37 through 42 removed outlier: 4.648A pdb=" N THR C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 53 through 60 Processing helix chain 'C' and resid 61 through 82 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.832A pdb=" N ASN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 218 through 227 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.319A pdb=" N VAL C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 362 Processing helix chain 'C' and resid 378 through 384 removed outlier: 3.544A pdb=" N LYS C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 438 through 451 Processing helix chain 'C' and resid 470 through 481 removed outlier: 3.951A pdb=" N MET C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'C' and resid 488 through 505 removed outlier: 3.599A pdb=" N LYS C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 529 removed outlier: 4.648A pdb=" N GLN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 581 through 591 removed outlier: 4.963A pdb=" N PHE C 587 " --> pdb=" O ASP C 583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.939A pdb=" N ASN A 279 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.611A pdb=" N ARG A 425 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 541 Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 276 removed outlier: 3.939A pdb=" N ASN B 279 " --> pdb=" O TYR B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AB4, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.612A pdb=" N ARG B 425 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AB6, first strand: chain 'B' and resid 533 through 541 Processing sheet with id=AB7, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AB8, first strand: chain 'C' and resid 275 through 276 removed outlier: 3.939A pdb=" N ASN C 279 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 312 through 313 Processing sheet with id=AC1, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.611A pdb=" N ARG C 425 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 432 through 433 Processing sheet with id=AC3, first strand: chain 'C' and resid 533 through 541 666 hydrogen bonds defined for protein. 1845 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: 11.81 Time building geometry restraints manager: 24.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 14631 1.13 - 1.31: 2707 1.31 - 1.49: 6372 1.49 - 1.67: 5672 1.67 - 1.85: 138 Bond restraints: 29520 Sorted by residual: bond pdb=" NH2 ARG A 211 " pdb="HH21 ARG A 211 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" NH2 ARG B 211 " pdb="HH21 ARG B 211 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" NE ARG A 201 " pdb=" HE ARG A 201 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" NH2 ARG C 211 " pdb="HH21 ARG C 211 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.57e+01 bond pdb=" NE ARG B 201 " pdb=" HE ARG B 201 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.56e+01 ... (remaining 29515 not shown) Histogram of bond angle deviations from ideal: 70.27 - 87.70: 174 87.70 - 105.13: 480 105.13 - 122.56: 50602 122.56 - 139.99: 2018 139.99 - 157.42: 87 Bond angle restraints: 53361 Sorted by residual: angle pdb=" C ASP B 309 " pdb=" N ILE B 310 " pdb=" CA ILE B 310 " ideal model delta sigma weight residual 122.59 147.14 -24.55 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C ASP A 309 " pdb=" N ILE A 310 " pdb=" CA ILE A 310 " ideal model delta sigma weight residual 122.59 147.14 -24.55 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C ASP C 309 " pdb=" N ILE C 310 " pdb=" CA ILE C 310 " ideal model delta sigma weight residual 122.59 147.12 -24.53 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C SER B 6 " pdb=" N ILE B 7 " pdb=" CA ILE B 7 " ideal model delta sigma weight residual 122.37 157.42 -35.05 1.29e+00 6.01e-01 7.38e+02 angle pdb=" C SER C 6 " pdb=" N ILE C 7 " pdb=" CA ILE C 7 " ideal model delta sigma weight residual 122.37 157.41 -35.04 1.29e+00 6.01e-01 7.38e+02 ... (remaining 53356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 13374 17.28 - 34.55: 401 34.55 - 51.83: 139 51.83 - 69.11: 39 69.11 - 86.39: 6 Dihedral angle restraints: 13959 sinusoidal: 7584 harmonic: 6375 Sorted by residual: dihedral pdb=" C PHE C 474 " pdb=" N PHE C 474 " pdb=" CA PHE C 474 " pdb=" CB PHE C 474 " ideal model delta harmonic sigma weight residual -122.60 -113.90 -8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C PHE A 474 " pdb=" N PHE A 474 " pdb=" CA PHE A 474 " pdb=" CB PHE A 474 " ideal model delta harmonic sigma weight residual -122.60 -113.92 -8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C PHE B 474 " pdb=" N PHE B 474 " pdb=" CA PHE B 474 " pdb=" CB PHE B 474 " ideal model delta harmonic sigma weight residual -122.60 -113.97 -8.63 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 13956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1156 0.064 - 0.129: 670 0.129 - 0.193: 323 0.193 - 0.257: 141 0.257 - 0.322: 23 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA PHE C 349 " pdb=" N PHE C 349 " pdb=" C PHE C 349 " pdb=" CB PHE C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA PHE A 349 " pdb=" N PHE A 349 " pdb=" C PHE A 349 " pdb=" CB PHE A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PHE B 349 " pdb=" N PHE B 349 " pdb=" C PHE B 349 " pdb=" CB PHE B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2310 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.31e+01 pdb=" CG TRP C 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP C 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 373 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 373 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP C 373 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP C 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 373 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP C 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP C 373 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP C 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP C 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP C 373 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.30e+01 pdb=" CG TRP A 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 373 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 373 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP A 373 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP A 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 373 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP A 373 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP A 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP A 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP A 373 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.30e+01 pdb=" CG TRP B 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 373 " -0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP B 373 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP B 373 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP B 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 373 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP B 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP B 373 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP B 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP B 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP B 373 " 0.043 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1719 2.13 - 2.75: 51445 2.75 - 3.37: 87024 3.37 - 3.98: 116701 3.98 - 4.60: 173952 Nonbonded interactions: 430841 Sorted by model distance: nonbonded pdb=" H THR B 137 " pdb=" HG1 THR B 137 " model vdw 1.515 2.100 nonbonded pdb=" H THR C 137 " pdb=" HG1 THR C 137 " model vdw 1.515 2.100 nonbonded pdb=" H THR A 137 " pdb=" HG1 THR A 137 " model vdw 1.515 2.100 nonbonded pdb=" H VAL C 182 " pdb=" HA VAL C 182 " model vdw 1.525 1.816 nonbonded pdb=" H VAL B 182 " pdb=" HA VAL B 182 " model vdw 1.525 1.816 ... (remaining 430836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.440 Extract box with map and model: 8.190 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 95.080 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4235 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 : 0.020 0.176 14877 Z= 1.276 Angle : 2.624 35.398 20166 Z= 1.814 Chirality : 0.102 0.322 2313 Planarity : 0.010 0.054 2568 Dihedral : 9.975 86.385 5556 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.04 (0.19), residues: 1791 helix: -1.52 (0.15), residues: 816 sheet: 2.08 (0.42), residues: 135 loop : 1.68 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.037 TRP A 373 HIS 0.022 0.003 HIS A 117 PHE 0.040 0.006 PHE C 261 TYR 0.059 0.010 TYR C 173 ARG 0.013 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7928 (tttt) cc_final: 0.7284 (tttm) REVERT: A 75 ASN cc_start: 0.7486 (m-40) cc_final: 0.7115 (m-40) REVERT: A 270 ASP cc_start: 0.7225 (t0) cc_final: 0.6498 (m-30) REVERT: B 41 LYS cc_start: 0.8089 (tttt) cc_final: 0.7428 (tttm) REVERT: B 75 ASN cc_start: 0.7415 (m-40) cc_final: 0.7150 (m-40) REVERT: B 270 ASP cc_start: 0.7179 (t0) cc_final: 0.6546 (m-30) REVERT: C 9 THR cc_start: 0.8251 (p) cc_final: 0.8031 (m) REVERT: C 41 LYS cc_start: 0.7978 (tttt) cc_final: 0.7691 (tttm) REVERT: C 270 ASP cc_start: 0.6936 (t0) cc_final: 0.6284 (m-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.6057 time to fit residues: 290.7422 Evaluate side-chains 278 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4335 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14877 Z= 0.279 Angle : 1.112 20.990 20166 Z= 0.678 Chirality : 0.045 0.152 2313 Planarity : 0.005 0.045 2568 Dihedral : 5.033 25.083 1971 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.36 % Allowed : 5.05 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.55 (0.20), residues: 1791 helix: -0.35 (0.17), residues: 807 sheet: 1.70 (0.45), residues: 129 loop : 1.16 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP C 373 HIS 0.008 0.002 HIS A 128 PHE 0.026 0.003 PHE B 352 TYR 0.024 0.002 TYR A 264 ARG 0.003 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 288 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7387 (m-40) cc_final: 0.7008 (m-40) REVERT: A 270 ASP cc_start: 0.7087 (t0) cc_final: 0.6499 (m-30) REVERT: A 347 LYS cc_start: 0.6545 (mttp) cc_final: 0.6339 (ttmt) REVERT: A 396 CYS cc_start: 0.8210 (m) cc_final: 0.7908 (m) REVERT: B 75 ASN cc_start: 0.7422 (m-40) cc_final: 0.7162 (m-40) REVERT: B 260 MET cc_start: 0.5272 (mmt) cc_final: 0.4910 (mmp) REVERT: B 270 ASP cc_start: 0.7383 (t0) cc_final: 0.6575 (m-30) REVERT: B 396 CYS cc_start: 0.8031 (m) cc_final: 0.7819 (m) REVERT: C 75 ASN cc_start: 0.7281 (m-40) cc_final: 0.6996 (m-40) REVERT: C 270 ASP cc_start: 0.7054 (t0) cc_final: 0.6489 (m-30) REVERT: C 396 CYS cc_start: 0.7897 (m) cc_final: 0.7664 (m) outliers start: 6 outliers final: 3 residues processed: 291 average time/residue: 0.5846 time to fit residues: 252.9272 Evaluate side-chains 272 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 269 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain C residue 305 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 161 optimal weight: 0.0980 chunk 173 optimal weight: 0.3980 chunk 143 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 129 optimal weight: 0.0770 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4289 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14877 Z= 0.174 Angle : 1.059 22.589 20166 Z= 0.644 Chirality : 0.043 0.139 2313 Planarity : 0.004 0.050 2568 Dihedral : 4.613 23.348 1971 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.36 % Allowed : 6.86 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.75 (0.20), residues: 1791 helix: -0.11 (0.17), residues: 819 sheet: 1.64 (0.45), residues: 129 loop : 1.24 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP C 373 HIS 0.003 0.001 HIS A 319 PHE 0.031 0.002 PHE B 477 TYR 0.020 0.001 TYR B 296 ARG 0.002 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 280 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASP cc_start: 0.7034 (t0) cc_final: 0.6553 (m-30) REVERT: A 363 THR cc_start: 0.7067 (p) cc_final: 0.6854 (t) REVERT: B 270 ASP cc_start: 0.7182 (t0) cc_final: 0.6577 (m-30) REVERT: C 91 THR cc_start: 0.7242 (m) cc_final: 0.6847 (p) REVERT: C 270 ASP cc_start: 0.7170 (t0) cc_final: 0.6557 (m-30) REVERT: C 576 LYS cc_start: 0.5713 (mttt) cc_final: 0.5370 (mmmt) outliers start: 6 outliers final: 2 residues processed: 285 average time/residue: 0.5776 time to fit residues: 244.5972 Evaluate side-chains 273 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 271 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain C residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4421 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14877 Z= 0.252 Angle : 1.060 22.206 20166 Z= 0.643 Chirality : 0.043 0.156 2313 Planarity : 0.004 0.055 2568 Dihedral : 4.601 23.918 1971 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.90 % Allowed : 6.56 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.49 (0.20), residues: 1791 helix: -0.09 (0.18), residues: 798 sheet: 1.20 (0.44), residues: 135 loop : 0.84 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 373 HIS 0.007 0.001 HIS B 117 PHE 0.030 0.002 PHE B 477 TYR 0.016 0.002 TYR B 296 ARG 0.003 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 265 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7417 (m-40) cc_final: 0.7038 (m-40) REVERT: B 97 ILE cc_start: 0.7725 (mt) cc_final: 0.7522 (mt) REVERT: B 270 ASP cc_start: 0.7027 (t0) cc_final: 0.6410 (m-30) REVERT: B 396 CYS cc_start: 0.8399 (m) cc_final: 0.8171 (m) REVERT: C 71 LYS cc_start: 0.6892 (tptt) cc_final: 0.6533 (tptt) REVERT: C 75 ASN cc_start: 0.7326 (m-40) cc_final: 0.7035 (m-40) REVERT: C 91 THR cc_start: 0.7339 (m) cc_final: 0.6848 (p) REVERT: C 260 MET cc_start: 0.6035 (mmp) cc_final: 0.5747 (mmt) REVERT: C 396 CYS cc_start: 0.8052 (m) cc_final: 0.7849 (m) outliers start: 15 outliers final: 12 residues processed: 273 average time/residue: 0.6129 time to fit residues: 253.4448 Evaluate side-chains 264 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4507 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14877 Z= 0.274 Angle : 1.064 22.289 20166 Z= 0.644 Chirality : 0.044 0.159 2313 Planarity : 0.004 0.056 2568 Dihedral : 4.595 24.724 1971 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.32 % Allowed : 7.64 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.08 (0.20), residues: 1791 helix: -0.33 (0.17), residues: 822 sheet: 0.87 (0.47), residues: 135 loop : 0.57 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 373 HIS 0.005 0.001 HIS B 117 PHE 0.032 0.002 PHE B 290 TYR 0.018 0.002 TYR B 296 ARG 0.004 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 261 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.7353 (m) cc_final: 0.6949 (p) REVERT: B 91 THR cc_start: 0.7320 (m) cc_final: 0.6856 (p) REVERT: B 270 ASP cc_start: 0.7119 (t0) cc_final: 0.6380 (m-30) REVERT: B 396 CYS cc_start: 0.8449 (m) cc_final: 0.8202 (m) REVERT: C 91 THR cc_start: 0.7339 (m) cc_final: 0.6839 (p) REVERT: C 396 CYS cc_start: 0.8311 (m) cc_final: 0.8080 (m) outliers start: 22 outliers final: 15 residues processed: 274 average time/residue: 0.5614 time to fit residues: 230.9639 Evaluate side-chains 270 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 33 optimal weight: 0.0270 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN B 89 ASN C 89 ASN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4502 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14877 Z= 0.223 Angle : 1.045 22.418 20166 Z= 0.634 Chirality : 0.043 0.152 2313 Planarity : 0.004 0.053 2568 Dihedral : 4.473 23.937 1971 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.26 % Allowed : 8.97 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.16 (0.20), residues: 1791 helix: -0.24 (0.18), residues: 819 sheet: 0.82 (0.48), residues: 135 loop : 0.59 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 373 HIS 0.005 0.001 HIS B 128 PHE 0.036 0.002 PHE B 290 TYR 0.025 0.002 TYR A 381 ARG 0.004 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 263 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.6839 (mmm) cc_final: 0.6304 (tmm) REVERT: B 270 ASP cc_start: 0.7051 (t0) cc_final: 0.6385 (m-30) REVERT: B 396 CYS cc_start: 0.8489 (m) cc_final: 0.8235 (m) REVERT: C 396 CYS cc_start: 0.8340 (m) cc_final: 0.8082 (m) outliers start: 21 outliers final: 17 residues processed: 275 average time/residue: 0.5823 time to fit residues: 243.3212 Evaluate side-chains 272 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4604 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14877 Z= 0.350 Angle : 1.087 22.167 20166 Z= 0.657 Chirality : 0.045 0.183 2313 Planarity : 0.005 0.043 2568 Dihedral : 4.724 25.282 1971 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.62 % Allowed : 9.51 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.45 (0.20), residues: 1791 helix: -0.58 (0.17), residues: 822 sheet: 0.58 (0.49), residues: 135 loop : 0.07 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 373 HIS 0.007 0.002 HIS A 128 PHE 0.036 0.003 PHE C 352 TYR 0.027 0.002 TYR A 381 ARG 0.005 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 255 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 ASP cc_start: 0.6947 (t0) cc_final: 0.6171 (m-30) REVERT: B 296 TYR cc_start: 0.6871 (m-80) cc_final: 0.6623 (m-80) REVERT: C 396 CYS cc_start: 0.8504 (m) cc_final: 0.8221 (m) outliers start: 27 outliers final: 25 residues processed: 266 average time/residue: 0.5509 time to fit residues: 220.0232 Evaluate side-chains 273 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 248 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4570 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14877 Z= 0.249 Angle : 1.056 22.278 20166 Z= 0.640 Chirality : 0.044 0.185 2313 Planarity : 0.004 0.042 2568 Dihedral : 4.608 24.496 1971 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.38 % Allowed : 10.23 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.28 (0.20), residues: 1791 helix: -0.43 (0.18), residues: 819 sheet: 0.71 (0.50), residues: 129 loop : 0.14 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 373 HIS 0.005 0.001 HIS C 117 PHE 0.029 0.002 PHE C 477 TYR 0.027 0.002 TYR A 381 ARG 0.005 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 251 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 ASP cc_start: 0.6860 (t0) cc_final: 0.6144 (m-30) REVERT: C 252 MET cc_start: 0.5451 (ttm) cc_final: 0.5049 (tpt) outliers start: 23 outliers final: 20 residues processed: 264 average time/residue: 0.5643 time to fit residues: 224.0092 Evaluate side-chains 268 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 248 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 0.3980 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4549 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14877 Z= 0.212 Angle : 1.048 22.117 20166 Z= 0.635 Chirality : 0.043 0.189 2313 Planarity : 0.004 0.044 2568 Dihedral : 4.505 23.960 1971 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.26 % Allowed : 10.83 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.16 (0.20), residues: 1791 helix: -0.31 (0.18), residues: 819 sheet: 0.88 (0.51), residues: 129 loop : 0.16 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 373 HIS 0.004 0.001 HIS C 117 PHE 0.033 0.002 PHE B 477 TYR 0.028 0.001 TYR A 381 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 250 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASP cc_start: 0.8480 (m-30) cc_final: 0.8264 (m-30) REVERT: B 270 ASP cc_start: 0.6837 (t0) cc_final: 0.6120 (m-30) REVERT: B 541 MET cc_start: 0.1158 (ttp) cc_final: 0.0595 (ttp) REVERT: C 91 THR cc_start: 0.7408 (m) cc_final: 0.6842 (p) REVERT: C 252 MET cc_start: 0.5446 (ttm) cc_final: 0.5058 (tpt) outliers start: 21 outliers final: 18 residues processed: 264 average time/residue: 0.5817 time to fit residues: 233.3832 Evaluate side-chains 267 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 249 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.0470 chunk 79 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4560 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14877 Z= 0.226 Angle : 1.051 22.130 20166 Z= 0.637 Chirality : 0.044 0.192 2313 Planarity : 0.004 0.046 2568 Dihedral : 4.513 23.830 1971 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.26 % Allowed : 10.95 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.16 (0.20), residues: 1791 helix: -0.32 (0.18), residues: 816 sheet: 0.93 (0.49), residues: 135 loop : 0.16 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 373 HIS 0.004 0.001 HIS C 117 PHE 0.035 0.002 PHE B 477 TYR 0.029 0.002 TYR A 381 ARG 0.005 0.000 ARG C 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 256 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASP cc_start: 0.8475 (m-30) cc_final: 0.8261 (m-30) REVERT: B 270 ASP cc_start: 0.6616 (t0) cc_final: 0.5965 (m-30) REVERT: B 541 MET cc_start: 0.1136 (ttp) cc_final: 0.0591 (ttp) REVERT: C 91 THR cc_start: 0.7376 (m) cc_final: 0.6785 (p) REVERT: C 168 ASN cc_start: 0.4985 (m-40) cc_final: 0.3736 (p0) REVERT: C 252 MET cc_start: 0.5471 (ttm) cc_final: 0.5080 (tpt) REVERT: C 389 MET cc_start: 0.6178 (ttm) cc_final: 0.5960 (ttm) outliers start: 21 outliers final: 21 residues processed: 270 average time/residue: 0.5530 time to fit residues: 227.3502 Evaluate side-chains 273 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 252 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.285092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.233400 restraints weight = 51276.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.243476 restraints weight = 23341.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.249611 restraints weight = 14817.914| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14877 Z= 0.204 Angle : 1.046 22.243 20166 Z= 0.634 Chirality : 0.043 0.191 2313 Planarity : 0.004 0.046 2568 Dihedral : 4.463 23.356 1971 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.02 % Allowed : 11.55 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.05 (0.21), residues: 1791 helix: -0.22 (0.18), residues: 810 sheet: 1.06 (0.49), residues: 135 loop : 0.17 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 373 HIS 0.004 0.001 HIS C 117 PHE 0.044 0.002 PHE A 290 TYR 0.035 0.001 TYR C 381 ARG 0.005 0.000 ARG C 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6700.84 seconds wall clock time: 118 minutes 45.83 seconds (7125.83 seconds total)