Starting phenix.real_space_refine on Wed Feb 14 12:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2024/7oji_12952_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2024/7oji_12952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2024/7oji_12952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2024/7oji_12952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2024/7oji_12952_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oji_12952/02_2024/7oji_12952_trim_updated.pdb" } resolution = 3.4 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= 0.040 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 8 5.49 5 S 58 5.16 5 C 5997 2.51 5 N 1483 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9195 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4453 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 3 Chain: "B" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4453 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 3 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1, 'TTC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.52, per 1000 atoms: 0.60 Number of scatterers: 9195 At special positions: 0 Unit cell: (100.98, 91.74, 128.04, 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 8 15.00 O 1649 8.00 N 1483 7.00 C 5997 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=2.02 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: 3.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 58.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' 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: 3.828A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.563A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.607A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 4.506A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 removed outlier: 3.577A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 420 through 461 removed outlier: 4.076A pdb=" N ILE A 423 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 440 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 441 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 442 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 461 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.654A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.757A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.819A 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 534 through 551 removed outlier: 3.976A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.529A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.608A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.873A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' 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: 3.829A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 4.564A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.606A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.506A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.576A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 340 through 352 Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 420 through 461 removed outlier: 4.076A pdb=" N ILE B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 427 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 440 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 441 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 442 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B 443 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 451 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 461 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 478 through 497 removed outlier: 3.653A pdb=" N ARG B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.757A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.820A 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 534 through 551 removed outlier: 3.976A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.528A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 3.607A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 600 Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.874A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.557A pdb=" N GLY A 69 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.918A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 242 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY A 80 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.557A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.917A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 242 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY B 80 " --> pdb=" O ILE B 242 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1086 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: 2.53 Time building geometry restraints manager: 4.21 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: 1414 1.31 - 1.44: 2486 1.44 - 1.57: 5370 1.57 - 1.69: 37 1.69 - 1.82: 94 Bond restraints: 9401 Sorted by residual: bond pdb=" C5 ATP A 705 " pdb=" N7 ATP A 705 " ideal model delta sigma weight residual 1.387 1.524 -0.137 1.00e-02 1.00e+04 1.88e+02 bond pdb=" C5 ATP B 704 " pdb=" N7 ATP B 704 " ideal model delta sigma weight residual 1.387 1.524 -0.137 1.00e-02 1.00e+04 1.86e+02 bond pdb=" C6 ATP B 704 " pdb=" N6 ATP B 704 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.06e+02 bond pdb=" C6 ATP A 705 " pdb=" N6 ATP A 705 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C4 ATP B 704 " pdb=" N9 ATP B 704 " ideal model delta sigma weight residual 1.374 1.272 0.102 1.00e-02 1.00e+04 1.04e+02 ... (remaining 9396 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.53: 276 106.53 - 114.80: 5760 114.80 - 123.07: 6307 123.07 - 131.34: 393 131.34 - 139.61: 17 Bond angle restraints: 12753 Sorted by residual: angle pdb=" PB ATP B 704 " pdb=" O3B ATP B 704 " pdb=" PG ATP B 704 " ideal model delta sigma weight residual 139.87 121.04 18.83 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP A 705 " pdb=" O3B ATP A 705 " pdb=" PG ATP A 705 " ideal model delta sigma weight residual 139.87 122.31 17.56 1.00e+00 1.00e+00 3.08e+02 angle pdb=" C4 ATP B 704 " pdb=" N9 ATP B 704 " pdb=" C8 ATP B 704 " ideal model delta sigma weight residual 105.72 121.81 -16.09 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C4 ATP A 705 " pdb=" N9 ATP A 705 " pdb=" C8 ATP A 705 " ideal model delta sigma weight residual 105.72 121.70 -15.98 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP B 704 " pdb=" O3A ATP B 704 " pdb=" PB ATP B 704 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 ... (remaining 12748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 5503 21.49 - 42.97: 274 42.97 - 64.46: 32 64.46 - 85.94: 9 85.94 - 107.43: 4 Dihedral angle restraints: 5822 sinusoidal: 2526 harmonic: 3296 Sorted by residual: dihedral pdb=" CA HIS B 283 " pdb=" C HIS B 283 " pdb=" N CYS B 284 " pdb=" CA CYS B 284 " ideal model delta harmonic sigma weight residual -180.00 -146.86 -33.14 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA HIS A 283 " pdb=" C HIS A 283 " pdb=" N CYS A 284 " pdb=" CA CYS A 284 " ideal model delta harmonic sigma weight residual -180.00 -146.92 -33.08 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA VAL B 493 " pdb=" C VAL B 493 " pdb=" N TYR B 494 " pdb=" CA TYR B 494 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.323: 1461 0.323 - 0.647: 4 0.647 - 0.970: 0 0.970 - 1.294: 0 1.294 - 1.617: 2 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CG LEU B 595 " pdb=" CB LEU B 595 " pdb=" CD1 LEU B 595 " pdb=" CD2 LEU B 595 " both_signs ideal model delta sigma weight residual False -2.59 -0.97 -1.62 2.00e-01 2.50e+01 6.54e+01 chirality pdb=" CG LEU A 595 " pdb=" CB LEU A 595 " pdb=" CD1 LEU A 595 " pdb=" CD2 LEU A 595 " both_signs ideal model delta sigma weight residual False -2.59 -0.97 -1.62 2.00e-01 2.50e+01 6.52e+01 chirality pdb=" C21 TTC A 701 " pdb=" C16 TTC A 701 " pdb=" C20 TTC A 701 " pdb=" O24 TTC A 701 " both_signs ideal model delta sigma weight residual False -2.50 -2.98 0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 1464 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 TTC A 701 " 0.009 2.00e-02 2.50e+03 1.08e-02 6.46e+00 pdb=" C11 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C13 TTC A 701 " 0.009 2.00e-02 2.50e+03 pdb=" C14 TTC A 701 " 0.008 2.00e-02 2.50e+03 pdb=" C15 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C16 TTC A 701 " 0.019 2.00e-02 2.50e+03 pdb=" C17 TTC A 701 " 0.007 2.00e-02 2.50e+03 pdb=" C19 TTC A 701 " -0.007 2.00e-02 2.50e+03 pdb=" C2 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C21 TTC A 701 " -0.033 2.00e-02 2.50e+03 pdb=" C27 TTC A 701 " -0.022 2.00e-02 2.50e+03 pdb=" C3 TTC A 701 " 0.010 2.00e-02 2.50e+03 pdb=" C4 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C5 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C6 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C7 TTC A 701 " -0.005 2.00e-02 2.50e+03 pdb=" C8 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C9 TTC A 701 " -0.002 2.00e-02 2.50e+03 pdb=" N10 TTC A 701 " -0.007 2.00e-02 2.50e+03 pdb=" N12 TTC A 701 " 0.006 2.00e-02 2.50e+03 pdb=" O18 TTC A 701 " -0.001 2.00e-02 2.50e+03 pdb=" O26 TTC A 701 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 211 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 212 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 211 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 212 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " -0.020 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1829 2.77 - 3.30: 9251 3.30 - 3.83: 14408 3.83 - 4.37: 17239 4.37 - 4.90: 30144 Nonbonded interactions: 72871 Sorted by model distance: nonbonded pdb=" O GLY B 594 " pdb=" OG1 THR B 598 " model vdw 2.231 2.440 nonbonded pdb=" O GLY A 594 " pdb=" OG1 THR A 598 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR B 123 " model vdw 2.297 2.440 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 123 " model vdw 2.298 2.440 nonbonded pdb=" O TYR B 336 " pdb=" OG SER B 339 " model vdw 2.312 2.440 ... (remaining 72866 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' and (resid 34 through 654 or resid 702 through 703)) selection = (chain 'B' and (resid 34 through 654 or resid 702 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.390 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: 0.000 Extract box with map and model: 11.930 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.120 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.012 0.195 9401 Z= 0.826 Angle : 1.079 18.833 12753 Z= 0.646 Chirality : 0.080 1.617 1467 Planarity : 0.004 0.037 1542 Dihedral : 12.846 107.428 3697 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 0.41 % Allowed : 2.46 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.15 (0.24), residues: 1128 helix: 1.03 (0.19), residues: 672 sheet: -1.28 (0.50), residues: 82 loop : -1.91 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 379 HIS 0.004 0.001 HIS B 267 PHE 0.014 0.001 PHE A 448 TYR 0.014 0.002 TYR B 282 ARG 0.003 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.067 Fit side-chains REVERT: B 231 MET cc_start: 0.8750 (ttm) cc_final: 0.8520 (ttm) outliers start: 4 outliers final: 3 residues processed: 182 average time/residue: 0.2657 time to fit residues: 65.3510 Evaluate side-chains 92 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 436 ASN B 162 ASN B 436 ASN B 457 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9401 Z= 0.185 Angle : 0.563 11.336 12753 Z= 0.293 Chirality : 0.040 0.176 1467 Planarity : 0.005 0.032 1542 Dihedral : 10.720 84.240 1649 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 1.84 % Allowed : 8.81 % Favored : 89.34 % 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: 0.03 (0.25), residues: 1128 helix: 1.06 (0.20), residues: 676 sheet: -0.84 (0.50), residues: 76 loop : -1.68 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE B 385 TYR 0.014 0.001 TYR A 282 ARG 0.003 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.085 Fit side-chains REVERT: A 131 MET cc_start: 0.7705 (tpp) cc_final: 0.7298 (tpp) REVERT: A 226 LEU cc_start: 0.8404 (pp) cc_final: 0.8166 (pp) REVERT: A 287 TYR cc_start: 0.7535 (m-80) cc_final: 0.7286 (m-80) REVERT: B 71 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6455 (mtp) outliers start: 18 outliers final: 8 residues processed: 104 average time/residue: 0.1940 time to fit residues: 29.6594 Evaluate side-chains 87 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 604 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9401 Z= 0.344 Angle : 0.604 12.635 12753 Z= 0.312 Chirality : 0.043 0.227 1467 Planarity : 0.005 0.037 1542 Dihedral : 10.492 88.794 1645 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.56 % Allowed : 10.35 % 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: -0.17 (0.25), residues: 1128 helix: 0.89 (0.20), residues: 670 sheet: -0.45 (0.51), residues: 76 loop : -1.83 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 379 HIS 0.006 0.002 HIS B 630 PHE 0.014 0.002 PHE B 293 TYR 0.012 0.001 TYR B 459 ARG 0.004 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.063 Fit side-chains REVERT: A 71 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7070 (mtp) REVERT: A 131 MET cc_start: 0.8018 (tpp) cc_final: 0.7594 (tpp) REVERT: A 226 LEU cc_start: 0.8508 (pp) cc_final: 0.8212 (pp) REVERT: A 287 TYR cc_start: 0.7488 (m-80) cc_final: 0.7286 (m-80) REVERT: B 125 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8850 (p) REVERT: B 525 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8483 (mp) outliers start: 25 outliers final: 11 residues processed: 109 average time/residue: 0.1848 time to fit residues: 29.7855 Evaluate side-chains 94 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 604 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS B 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9401 Z= 0.173 Angle : 0.500 7.751 12753 Z= 0.262 Chirality : 0.039 0.172 1467 Planarity : 0.004 0.033 1542 Dihedral : 10.130 88.825 1645 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.25 % Allowed : 11.78 % Favored : 85.96 % 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: 0.12 (0.25), residues: 1128 helix: 1.01 (0.20), residues: 682 sheet: -0.17 (0.53), residues: 76 loop : -1.62 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.010 0.001 PHE B 591 TYR 0.013 0.001 TYR A 282 ARG 0.002 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.961 Fit side-chains REVERT: A 131 MET cc_start: 0.7946 (tpp) cc_final: 0.7518 (tpp) REVERT: A 226 LEU cc_start: 0.8465 (pp) cc_final: 0.8192 (pp) REVERT: A 386 LYS cc_start: 0.8463 (mttm) cc_final: 0.8262 (mttt) REVERT: A 495 PHE cc_start: 0.8066 (m-80) cc_final: 0.7847 (m-80) REVERT: B 71 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6428 (mtp) REVERT: B 388 LEU cc_start: 0.8867 (tp) cc_final: 0.8636 (tp) REVERT: B 614 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8666 (mp) outliers start: 22 outliers final: 13 residues processed: 101 average time/residue: 0.1737 time to fit residues: 26.1579 Evaluate side-chains 93 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9401 Z= 0.450 Angle : 0.636 8.260 12753 Z= 0.328 Chirality : 0.044 0.181 1467 Planarity : 0.005 0.036 1542 Dihedral : 10.332 83.345 1645 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.69 % Allowed : 11.27 % Favored : 85.04 % 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: -0.23 (0.25), residues: 1128 helix: 0.82 (0.20), residues: 674 sheet: -0.20 (0.55), residues: 76 loop : -1.92 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 627 HIS 0.008 0.002 HIS A 155 PHE 0.013 0.002 PHE B 293 TYR 0.012 0.002 TYR B 459 ARG 0.002 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 81 time to evaluate : 1.051 Fit side-chains REVERT: A 131 MET cc_start: 0.8208 (tpp) cc_final: 0.7704 (tpp) REVERT: A 226 LEU cc_start: 0.8552 (pp) cc_final: 0.8009 (mm) REVERT: B 525 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8443 (mp) REVERT: B 614 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8676 (mp) outliers start: 36 outliers final: 17 residues processed: 104 average time/residue: 0.1828 time to fit residues: 28.2463 Evaluate side-chains 95 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.0370 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS B 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9401 Z= 0.166 Angle : 0.488 9.478 12753 Z= 0.255 Chirality : 0.039 0.141 1467 Planarity : 0.004 0.032 1542 Dihedral : 9.684 78.035 1645 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 12.91 % Favored : 84.94 % 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: 0.15 (0.26), residues: 1128 helix: 1.10 (0.21), residues: 668 sheet: -0.02 (0.57), residues: 76 loop : -1.67 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.004 0.001 HIS A 457 PHE 0.009 0.001 PHE B 591 TYR 0.010 0.001 TYR A 336 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.332 Fit side-chains REVERT: A 226 LEU cc_start: 0.8489 (pp) cc_final: 0.7973 (mm) REVERT: B 71 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6419 (mtp) REVERT: B 468 SER cc_start: 0.8802 (m) cc_final: 0.8587 (t) REVERT: B 525 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8550 (mp) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 0.1866 time to fit residues: 26.6531 Evaluate side-chains 93 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 604 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9401 Z= 0.235 Angle : 0.515 10.116 12753 Z= 0.265 Chirality : 0.039 0.140 1467 Planarity : 0.004 0.031 1542 Dihedral : 9.599 76.354 1645 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.87 % Allowed : 12.50 % Favored : 84.63 % 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: 0.13 (0.26), residues: 1128 helix: 1.07 (0.21), residues: 674 sheet: 0.16 (0.57), residues: 76 loop : -1.74 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.008 0.001 HIS B 243 PHE 0.012 0.001 PHE A 506 TYR 0.010 0.001 TYR B 459 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 1.101 Fit side-chains REVERT: A 131 MET cc_start: 0.8013 (tpp) cc_final: 0.7525 (tpp) REVERT: A 226 LEU cc_start: 0.8521 (pp) cc_final: 0.7986 (mm) REVERT: B 468 SER cc_start: 0.8838 (m) cc_final: 0.8623 (t) REVERT: B 525 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8534 (mp) outliers start: 28 outliers final: 19 residues processed: 97 average time/residue: 0.1655 time to fit residues: 24.9490 Evaluate side-chains 97 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 604 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 105 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS B 243 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9401 Z= 0.140 Angle : 0.473 10.463 12753 Z= 0.244 Chirality : 0.037 0.147 1467 Planarity : 0.004 0.030 1542 Dihedral : 9.218 71.661 1645 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.36 % Allowed : 13.22 % Favored : 84.43 % 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: 0.40 (0.26), residues: 1128 helix: 1.28 (0.21), residues: 666 sheet: 0.33 (0.58), residues: 76 loop : -1.58 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.004 0.001 HIS A 155 PHE 0.009 0.001 PHE A 591 TYR 0.008 0.001 TYR B 459 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 1.015 Fit side-chains REVERT: A 131 MET cc_start: 0.7848 (tpp) cc_final: 0.7561 (tpp) REVERT: A 226 LEU cc_start: 0.8491 (pp) cc_final: 0.7948 (mm) REVERT: B 243 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7042 (t70) REVERT: B 468 SER cc_start: 0.8792 (m) cc_final: 0.8570 (t) REVERT: B 525 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8553 (mp) outliers start: 23 outliers final: 18 residues processed: 98 average time/residue: 0.1639 time to fit residues: 24.6331 Evaluate side-chains 99 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 604 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS B 243 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 9401 Z= 0.437 Angle : 0.625 11.222 12753 Z= 0.318 Chirality : 0.043 0.145 1467 Planarity : 0.005 0.030 1542 Dihedral : 9.671 75.519 1645 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.66 % Allowed : 13.42 % Favored : 83.91 % 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: -0.03 (0.25), residues: 1128 helix: 0.97 (0.21), residues: 674 sheet: 0.32 (0.58), residues: 76 loop : -1.90 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 627 HIS 0.027 0.003 HIS A 283 PHE 0.013 0.002 PHE B 142 TYR 0.016 0.001 TYR A 282 ARG 0.002 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 1.033 Fit side-chains REVERT: A 131 MET cc_start: 0.8064 (tpp) cc_final: 0.7625 (tpp) REVERT: A 226 LEU cc_start: 0.8552 (pp) cc_final: 0.8015 (mm) REVERT: B 243 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7217 (t70) REVERT: B 525 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 614 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8638 (mp) outliers start: 26 outliers final: 19 residues processed: 96 average time/residue: 0.1674 time to fit residues: 24.9540 Evaluate side-chains 100 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS B 243 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9401 Z= 0.223 Angle : 0.522 11.654 12753 Z= 0.267 Chirality : 0.039 0.144 1467 Planarity : 0.004 0.030 1542 Dihedral : 9.501 73.543 1645 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.25 % Allowed : 13.83 % Favored : 83.91 % 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: 0.13 (0.26), residues: 1128 helix: 1.06 (0.21), residues: 674 sheet: 0.52 (0.59), residues: 76 loop : -1.80 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.005 0.001 HIS B 243 PHE 0.008 0.001 PHE A 591 TYR 0.012 0.001 TYR B 459 ARG 0.002 0.000 ARG B 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.002 Fit side-chains REVERT: A 131 MET cc_start: 0.7979 (tpp) cc_final: 0.7608 (tpp) REVERT: A 226 LEU cc_start: 0.8528 (pp) cc_final: 0.8000 (mm) REVERT: B 243 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7460 (t70) REVERT: B 460 ILE cc_start: 0.7807 (mm) cc_final: 0.7547 (mt) REVERT: B 525 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8529 (mp) outliers start: 22 outliers final: 19 residues processed: 94 average time/residue: 0.1602 time to fit residues: 23.5992 Evaluate side-chains 99 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 283 HIS ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092746 restraints weight = 16636.494| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.89 r_work: 0.3135 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9401 Z= 0.156 Angle : 0.493 11.533 12753 Z= 0.252 Chirality : 0.038 0.143 1467 Planarity : 0.004 0.031 1542 Dihedral : 9.316 71.760 1645 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.15 % Allowed : 14.04 % Favored : 83.81 % 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: 0.35 (0.26), residues: 1128 helix: 1.24 (0.21), residues: 668 sheet: 0.59 (0.59), residues: 76 loop : -1.66 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.004 0.001 HIS A 155 PHE 0.008 0.001 PHE A 591 TYR 0.012 0.001 TYR B 459 ARG 0.002 0.000 ARG B 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.89 seconds wall clock time: 39 minutes 29.33 seconds (2369.33 seconds total)