Starting phenix.real_space_refine on Thu Mar 14 14:10:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bht_16069/03_2024/8bht_16069_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.046 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 P 6 5.49 5 S 58 5.16 5 C 5854 2.51 5 N 1472 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 3 Chain: "B" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 3 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ATP': 1, 'CLR': 1, 'R1H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.96, per 1000 atoms: 0.55 Number of scatterers: 9016 At special positions: 0 Unit cell: (92.4, 97.02, 121.44, 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 58 16.00 P 6 15.00 O 1626 8.00 N 1472 7.00 C 5854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 3.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 4 sheets defined 59.4% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 188 through 202 removed outlier: 5.041A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.686A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.214A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 4.331A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 392 through 412 Processing helix chain 'A' and resid 422 through 441 removed outlier: 3.805A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.901A pdb=" N PHE A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 449 " --> pdb=" O GLU A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 449' Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 496 removed outlier: 4.965A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix Proline residue: A 485 - end of helix removed outlier: 4.853A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 Processing helix chain 'A' and resid 535 through 550 Processing helix chain 'A' and resid 553 through 556 No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.373A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 571' Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.770A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 188 through 202 removed outlier: 5.042A pdb=" N THR B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.685A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.214A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.331A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 340 through 353 Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 392 through 412 Processing helix chain 'B' and resid 422 through 441 removed outlier: 3.805A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.901A pdb=" N PHE B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 449 " --> pdb=" O GLU B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 449' Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 496 removed outlier: 4.965A pdb=" N LEU B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Proline residue: B 480 - end of helix Proline residue: B 485 - end of helix removed outlier: 4.852A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 Processing helix chain 'B' and resid 535 through 550 Processing helix chain 'B' and resid 553 through 556 No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 563 through 571 removed outlier: 4.374A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 571' Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.770A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 75 through 78 removed outlier: 6.007A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.612A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.007A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.612A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1344 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: 2.45 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1395 1.31 - 1.43: 2508 1.43 - 1.56: 5199 1.56 - 1.69: 21 1.69 - 1.81: 94 Bond restraints: 9217 Sorted by residual: bond pdb=" C13 R1H B 703 " pdb=" N08 R1H B 703 " ideal model delta sigma weight residual 1.455 1.285 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.35e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.86e+01 ... (remaining 9212 not shown) Histogram of bond angle deviations from ideal: 98.47 - 106.03: 198 106.03 - 113.58: 5208 113.58 - 121.14: 4972 121.14 - 128.70: 2075 128.70 - 136.26: 47 Bond angle restraints: 12500 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 120.76 19.11 1.00e+00 1.00e+00 3.65e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 120.82 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 122.00 14.83 1.00e+00 1.00e+00 2.20e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 122.01 14.82 1.00e+00 1.00e+00 2.20e+02 angle pdb=" C5 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N3 ATP A 701 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.63e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 5266 21.46 - 42.92: 246 42.92 - 64.38: 39 64.38 - 85.84: 9 85.84 - 107.30: 2 Dihedral angle restraints: 5562 sinusoidal: 2288 harmonic: 3274 Sorted by residual: dihedral pdb=" CA GLN A 181 " pdb=" C GLN A 181 " pdb=" N PHE A 182 " pdb=" CA PHE A 182 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLN B 181 " pdb=" C GLN B 181 " pdb=" N PHE B 182 " pdb=" CA PHE B 182 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" C07 R1H B 703 " pdb=" C09 R1H B 703 " pdb=" N08 R1H B 703 " pdb=" C10 R1H B 703 " ideal model delta sinusoidal sigma weight residual -53.85 53.45 -107.30 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1308 0.069 - 0.139: 118 0.139 - 0.208: 7 0.208 - 0.277: 3 0.277 - 0.346: 2 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C17 CLR A 702 " pdb=" C13 CLR A 702 " pdb=" C16 CLR A 702 " pdb=" C20 CLR A 702 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C17 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C16 CLR B 702 " pdb=" C20 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C20 CLR B 702 " pdb=" C17 CLR B 702 " pdb=" C21 CLR B 702 " pdb=" C22 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.59 2.85 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1435 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 484 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 485 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 484 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 485 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 211 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.90e-01 pdb=" N PRO A 212 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.013 5.00e-02 4.00e+02 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2200 2.79 - 3.32: 9130 3.32 - 3.84: 14401 3.84 - 4.37: 17186 4.37 - 4.90: 29848 Nonbonded interactions: 72765 Sorted by model distance: nonbonded pdb=" OD1 ASP A 296 " pdb=" NH2 ARG B 246 " model vdw 2.260 2.520 nonbonded pdb=" N GLU A 611 " pdb=" OE1 GLU A 611 " model vdw 2.370 2.520 nonbonded pdb=" N GLU B 611 " pdb=" OE1 GLU B 611 " model vdw 2.371 2.520 nonbonded pdb=" OG SER A 384 " pdb=" OD1 ASP A 477 " model vdw 2.373 2.440 nonbonded pdb=" OG SER B 384 " pdb=" OD1 ASP B 477 " model vdw 2.373 2.440 ... (remaining 72760 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' and (resid 34 through 654 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.780 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.800 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 9217 Z= 0.539 Angle : 0.784 19.106 12500 Z= 0.515 Chirality : 0.045 0.346 1438 Planarity : 0.003 0.033 1534 Dihedral : 12.869 107.299 3453 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.32 % Favored : 97.50 % Rotamer: Outliers : 0.41 % Allowed : 5.58 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1122 helix: 1.50 (0.20), residues: 648 sheet: -1.71 (0.65), residues: 60 loop : -1.66 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 627 HIS 0.005 0.001 HIS A 267 PHE 0.012 0.001 PHE B 39 TYR 0.010 0.001 TYR A 463 ARG 0.004 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 587 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8530 (mp) REVERT: B 108 ILE cc_start: 0.8258 (pp) cc_final: 0.7937 (mt) outliers start: 4 outliers final: 0 residues processed: 181 average time/residue: 0.2382 time to fit residues: 57.5977 Evaluate side-chains 88 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 109 ASN B 126 GLN B 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9217 Z= 0.181 Angle : 0.577 10.131 12500 Z= 0.292 Chirality : 0.040 0.193 1438 Planarity : 0.004 0.039 1534 Dihedral : 8.817 89.786 1425 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 9.71 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1122 helix: 2.01 (0.21), residues: 668 sheet: -0.90 (0.57), residues: 82 loop : -1.37 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 564 HIS 0.004 0.001 HIS A 267 PHE 0.022 0.002 PHE A 293 TYR 0.012 0.001 TYR B 459 ARG 0.006 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8242 (pp) cc_final: 0.8012 (mt) REVERT: B 198 MET cc_start: 0.7964 (mtp) cc_final: 0.7754 (mtp) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.1596 time to fit residues: 27.4822 Evaluate side-chains 89 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9217 Z= 0.261 Angle : 0.565 8.786 12500 Z= 0.289 Chirality : 0.041 0.167 1438 Planarity : 0.004 0.035 1534 Dihedral : 8.288 80.532 1423 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 3.10 % Allowed : 9.40 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1122 helix: 2.10 (0.20), residues: 652 sheet: -0.65 (0.58), residues: 86 loop : -1.49 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS A 267 PHE 0.012 0.001 PHE B 511 TYR 0.011 0.001 TYR B 463 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: B 198 MET cc_start: 0.8030 (mtp) cc_final: 0.7720 (mtp) REVERT: B 654 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6483 (m-80) outliers start: 30 outliers final: 18 residues processed: 104 average time/residue: 0.1684 time to fit residues: 26.9073 Evaluate side-chains 91 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 96 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9217 Z= 0.165 Angle : 0.507 8.021 12500 Z= 0.259 Chirality : 0.038 0.149 1438 Planarity : 0.003 0.033 1534 Dihedral : 8.050 77.164 1423 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.17 % Allowed : 10.74 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1122 helix: 2.28 (0.21), residues: 652 sheet: -0.50 (0.59), residues: 86 loop : -1.40 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.000 HIS A 267 PHE 0.009 0.001 PHE B 432 TYR 0.010 0.001 TYR B 336 ARG 0.004 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: B 198 MET cc_start: 0.7890 (mtp) cc_final: 0.7535 (mtp) REVERT: B 654 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6580 (m-80) outliers start: 21 outliers final: 11 residues processed: 94 average time/residue: 0.1540 time to fit residues: 22.5136 Evaluate side-chains 83 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0970 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 629 ASN B 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9217 Z= 0.379 Angle : 0.635 10.964 12500 Z= 0.320 Chirality : 0.043 0.155 1438 Planarity : 0.004 0.036 1534 Dihedral : 8.007 74.996 1423 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.41 % Allowed : 10.02 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1122 helix: 1.84 (0.20), residues: 652 sheet: -0.68 (0.58), residues: 86 loop : -1.45 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 379 HIS 0.005 0.001 HIS A 267 PHE 0.017 0.002 PHE B 511 TYR 0.020 0.002 TYR B 463 ARG 0.003 0.001 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 0.935 Fit side-chains REVERT: B 654 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.6972 (m-10) outliers start: 33 outliers final: 23 residues processed: 102 average time/residue: 0.1681 time to fit residues: 26.1073 Evaluate side-chains 88 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9217 Z= 0.167 Angle : 0.527 9.829 12500 Z= 0.265 Chirality : 0.039 0.222 1438 Planarity : 0.003 0.034 1534 Dihedral : 7.876 79.961 1423 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.27 % Allowed : 12.19 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1122 helix: 2.14 (0.20), residues: 664 sheet: -0.51 (0.57), residues: 86 loop : -1.53 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.003 0.000 HIS A 267 PHE 0.011 0.001 PHE B 432 TYR 0.010 0.001 TYR B 336 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.992 Fit side-chains REVERT: B 127 ASP cc_start: 0.7230 (t0) cc_final: 0.6578 (m-30) REVERT: B 654 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7110 (m-10) outliers start: 22 outliers final: 13 residues processed: 92 average time/residue: 0.1626 time to fit residues: 23.1851 Evaluate side-chains 85 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.0570 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9217 Z= 0.168 Angle : 0.512 11.088 12500 Z= 0.255 Chirality : 0.038 0.266 1438 Planarity : 0.003 0.034 1534 Dihedral : 7.753 81.882 1423 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.58 % Allowed : 12.09 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1122 helix: 2.26 (0.20), residues: 666 sheet: -0.54 (0.56), residues: 86 loop : -1.41 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.002 0.000 HIS A 267 PHE 0.012 0.001 PHE B 294 TYR 0.010 0.001 TYR B 336 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 1.077 Fit side-chains REVERT: B 127 ASP cc_start: 0.7176 (t0) cc_final: 0.6494 (m-30) REVERT: B 654 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7652 (m-10) outliers start: 25 outliers final: 17 residues processed: 94 average time/residue: 0.1675 time to fit residues: 24.1329 Evaluate side-chains 88 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 0.0470 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.0030 overall best weight: 1.7492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9217 Z= 0.304 Angle : 0.594 11.595 12500 Z= 0.293 Chirality : 0.041 0.293 1438 Planarity : 0.004 0.035 1534 Dihedral : 7.752 78.726 1423 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.48 % Allowed : 12.09 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1122 helix: 2.04 (0.20), residues: 668 sheet: -0.64 (0.57), residues: 86 loop : -1.46 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS A 267 PHE 0.011 0.001 PHE B 511 TYR 0.013 0.001 TYR B 463 ARG 0.002 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 1.137 Fit side-chains REVERT: B 127 ASP cc_start: 0.7202 (t0) cc_final: 0.6546 (m-30) outliers start: 24 outliers final: 19 residues processed: 93 average time/residue: 0.1656 time to fit residues: 23.8556 Evaluate side-chains 90 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9217 Z= 0.183 Angle : 0.528 12.054 12500 Z= 0.261 Chirality : 0.039 0.308 1438 Planarity : 0.003 0.036 1534 Dihedral : 7.696 81.915 1423 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.27 % Allowed : 12.40 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1122 helix: 2.20 (0.20), residues: 668 sheet: -0.66 (0.57), residues: 86 loop : -1.38 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.000 HIS A 267 PHE 0.011 0.001 PHE B 432 TYR 0.011 0.001 TYR B 336 ARG 0.002 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 1.036 Fit side-chains REVERT: A 108 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 127 ASP cc_start: 0.7176 (t0) cc_final: 0.6555 (m-30) outliers start: 22 outliers final: 18 residues processed: 92 average time/residue: 0.1597 time to fit residues: 22.8500 Evaluate side-chains 89 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9217 Z= 0.376 Angle : 0.641 17.223 12500 Z= 0.316 Chirality : 0.043 0.344 1438 Planarity : 0.004 0.036 1534 Dihedral : 7.789 77.145 1423 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.48 % Allowed : 12.29 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1122 helix: 1.70 (0.20), residues: 684 sheet: -0.83 (0.57), residues: 86 loop : -1.47 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 PHE 0.014 0.002 PHE A 489 TYR 0.015 0.002 TYR B 463 ARG 0.003 0.000 ARG B 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.998 Fit side-chains REVERT: B 127 ASP cc_start: 0.7241 (t0) cc_final: 0.6641 (m-30) outliers start: 24 outliers final: 20 residues processed: 91 average time/residue: 0.1660 time to fit residues: 23.1943 Evaluate side-chains 91 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102842 restraints weight = 12701.744| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.53 r_work: 0.3220 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9217 Z= 0.191 Angle : 0.548 15.068 12500 Z= 0.269 Chirality : 0.039 0.339 1438 Planarity : 0.003 0.038 1534 Dihedral : 7.749 81.823 1423 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.96 % Allowed : 13.22 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1122 helix: 1.97 (0.20), residues: 684 sheet: -0.77 (0.57), residues: 86 loop : -1.33 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 PHE 0.012 0.001 PHE B 432 TYR 0.010 0.001 TYR B 336 ARG 0.002 0.000 ARG A 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.31 seconds wall clock time: 35 minutes 45.29 seconds (2145.29 seconds total)