Starting phenix.real_space_refine on Wed Feb 14 10:02:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/02_2024/7psd_13612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/02_2024/7psd_13612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/02_2024/7psd_13612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/02_2024/7psd_13612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/02_2024/7psd_13612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/02_2024/7psd_13612.pdb" } resolution = 3.0 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= -0.001 sd= 0.102 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5784 2.51 5 N 1574 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 485": "NH1" <-> "NH2" Residue "B PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" 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: 9032 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4516 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 17, 'TRANS': 562} Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4516 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 17, 'TRANS': 562} Time building chain proxies: 5.13, per 1000 atoms: 0.57 Number of scatterers: 9032 At special positions: 0 Unit cell: (118.976, 75.712, 141.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1650 8.00 N 1574 7.00 C 5784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 69.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.669A pdb=" N GLN B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 145 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 159 through 206 removed outlier: 3.750A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 240 Processing helix chain 'B' and resid 240 through 259 Processing helix chain 'B' and resid 260 through 309 removed outlier: 3.824A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 318 through 371 removed outlier: 3.504A pdb=" N GLU B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.662A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 398 removed outlier: 4.270A pdb=" N ASN B 395 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE B 396 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 392 through 398' Processing helix chain 'B' and resid 399 through 418 removed outlier: 3.742A pdb=" N ARG B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 removed outlier: 4.653A pdb=" N ARG B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 565 through 568 removed outlier: 4.052A pdb=" N GLN B 568 " --> pdb=" O HIS B 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 565 through 568' Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.937A pdb=" N ALA B 607 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 625 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.922A pdb=" N TYR B 642 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.554A pdb=" N GLU B 666 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 674 removed outlier: 4.033A pdb=" N GLU B 673 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 110 through 145 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 159 through 206 removed outlier: 3.749A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 240 Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 260 through 309 removed outlier: 3.823A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 371 removed outlier: 3.504A pdb=" N GLU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.661A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 removed outlier: 4.271A pdb=" N ASN A 395 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 396 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 398' Processing helix chain 'A' and resid 399 through 418 removed outlier: 3.743A pdb=" N ARG A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 4.653A pdb=" N ARG A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 565 through 568 removed outlier: 4.052A pdb=" N GLN A 568 " --> pdb=" O HIS A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.937A pdb=" N ALA A 607 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 625 Processing helix chain 'A' and resid 637 through 642 removed outlier: 3.923A pdb=" N TYR A 642 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.555A pdb=" N GLU A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.034A pdb=" N GLU A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 457 through 464 removed outlier: 5.296A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 462 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU B 444 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 464 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG B 442 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 446 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN B 495 " --> pdb=" O VAL B 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 517 through 519 removed outlier: 3.556A pdb=" N ILE B 647 " --> pdb=" O GLY B 659 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU B 657 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 529 through 530 Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 464 removed outlier: 5.296A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 462 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU A 444 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE A 464 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG A 442 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 446 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 495 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.556A pdb=" N ILE A 647 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU A 657 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530 612 hydrogen bonds defined for protein. 1800 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: 2.78 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2635 1.33 - 1.45: 1694 1.45 - 1.58: 4823 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 9196 Sorted by residual: bond pdb=" CB THR A 281 " pdb=" CG2 THR A 281 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.54e+01 bond pdb=" CB THR B 281 " pdb=" CG2 THR B 281 " ideal model delta sigma weight residual 1.521 1.392 0.129 3.30e-02 9.18e+02 1.53e+01 bond pdb=" C SER B 156 " pdb=" N ALA B 157 " ideal model delta sigma weight residual 1.332 1.287 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" C SER A 156 " pdb=" N ALA A 157 " ideal model delta sigma weight residual 1.332 1.288 0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" CG1 ILE A 192 " pdb=" CD1 ILE A 192 " ideal model delta sigma weight residual 1.513 1.392 0.121 3.90e-02 6.57e+02 9.60e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 95.14 - 102.96: 48 102.96 - 110.77: 3138 110.77 - 118.58: 4188 118.58 - 126.40: 4994 126.40 - 134.21: 102 Bond angle restraints: 12470 Sorted by residual: angle pdb=" CA TRP A 284 " pdb=" CB TRP A 284 " pdb=" CG TRP A 284 " ideal model delta sigma weight residual 113.60 121.87 -8.27 1.90e+00 2.77e-01 1.89e+01 angle pdb=" CA TRP B 284 " pdb=" CB TRP B 284 " pdb=" CG TRP B 284 " ideal model delta sigma weight residual 113.60 121.84 -8.24 1.90e+00 2.77e-01 1.88e+01 angle pdb=" N VAL B 400 " pdb=" CA VAL B 400 " pdb=" C VAL B 400 " ideal model delta sigma weight residual 110.36 114.48 -4.12 1.05e+00 9.07e-01 1.54e+01 angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" C VAL A 400 " ideal model delta sigma weight residual 110.36 114.48 -4.12 1.05e+00 9.07e-01 1.54e+01 angle pdb=" N VAL B 155 " pdb=" CA VAL B 155 " pdb=" C VAL B 155 " ideal model delta sigma weight residual 110.21 105.89 4.32 1.13e+00 7.83e-01 1.46e+01 ... (remaining 12465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4918 17.12 - 34.24: 485 34.24 - 51.36: 89 51.36 - 68.48: 10 68.48 - 85.59: 14 Dihedral angle restraints: 5516 sinusoidal: 2156 harmonic: 3360 Sorted by residual: dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N PRO B 452 " pdb=" CA PRO B 452 " ideal model delta harmonic sigma weight residual 180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA SER B 399 " pdb=" C SER B 399 " pdb=" N VAL B 400 " pdb=" CA VAL B 400 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1365 0.118 - 0.235: 97 0.235 - 0.353: 0 0.353 - 0.470: 0 0.470 - 0.588: 2 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CB ILE A 192 " pdb=" CA ILE A 192 " pdb=" CG1 ILE A 192 " pdb=" CG2 ILE A 192 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" CB ILE B 192 " pdb=" CA ILE B 192 " pdb=" CG1 ILE B 192 " pdb=" CG2 ILE B 192 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.61e+00 chirality pdb=" CA PHE A 355 " pdb=" N PHE A 355 " pdb=" C PHE A 355 " pdb=" CB PHE A 355 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1461 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 137 " 0.015 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE A 137 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 137 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE A 137 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 137 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 137 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 137 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 137 " -0.015 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE B 137 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE B 137 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE B 137 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 137 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 137 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 137 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " -0.031 2.00e-02 2.50e+03 1.97e-02 6.78e+00 pdb=" CG PHE B 388 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " -0.015 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 454 2.70 - 3.25: 9435 3.25 - 3.80: 14950 3.80 - 4.35: 18651 4.35 - 4.90: 31686 Nonbonded interactions: 75176 Sorted by model distance: nonbonded pdb=" O GLY A 566 " pdb=" OG1 THR A 569 " model vdw 2.146 2.440 nonbonded pdb=" O GLY B 566 " pdb=" OG1 THR B 569 " model vdw 2.146 2.440 nonbonded pdb=" O LEU A 586 " pdb=" OG SER A 589 " model vdw 2.290 2.440 nonbonded pdb=" O LEU B 586 " pdb=" OG SER B 589 " model vdw 2.290 2.440 nonbonded pdb=" O ARG B 637 " pdb=" OG1 THR B 640 " model vdw 2.302 2.440 ... (remaining 75171 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' } 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: 2.010 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: 7.480 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.040 Find NCS groups from input model: 0.460 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.015 0.130 9196 Z= 0.967 Angle : 1.115 12.813 12470 Z= 0.626 Chirality : 0.069 0.588 1464 Planarity : 0.006 0.056 1584 Dihedral : 14.392 85.594 3352 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -1.38 (0.23), residues: 1156 helix: -0.59 (0.17), residues: 750 sheet: -0.63 (0.68), residues: 56 loop : -1.37 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP B 284 HIS 0.004 0.001 HIS A 202 PHE 0.053 0.005 PHE A 137 TYR 0.017 0.003 TYR A 401 ARG 0.014 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.958 Fit side-chains REVERT: B 468 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7306 (mmpt) REVERT: B 621 ASN cc_start: 0.9158 (m-40) cc_final: 0.8475 (m110) REVERT: B 632 LEU cc_start: 0.8247 (mp) cc_final: 0.7948 (mp) outliers start: 0 outliers final: 1 residues processed: 123 average time/residue: 0.8140 time to fit residues: 110.8764 Evaluate side-chains 103 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9196 Z= 0.248 Angle : 0.627 7.489 12470 Z= 0.334 Chirality : 0.043 0.170 1464 Planarity : 0.004 0.045 1584 Dihedral : 5.151 22.193 1268 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.46 % Allowed : 9.98 % Favored : 88.57 % 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: 0.06 (0.25), residues: 1156 helix: 0.63 (0.18), residues: 754 sheet: -0.39 (0.68), residues: 56 loop : -1.03 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 284 HIS 0.003 0.001 HIS B 211 PHE 0.030 0.003 PHE B 388 TYR 0.010 0.001 TYR A 136 ARG 0.006 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.027 Fit side-chains REVERT: B 632 LEU cc_start: 0.8377 (mp) cc_final: 0.8109 (mp) REVERT: A 595 ASP cc_start: 0.7586 (t0) cc_final: 0.7353 (p0) REVERT: A 617 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7706 (tpt) outliers start: 14 outliers final: 6 residues processed: 108 average time/residue: 0.6606 time to fit residues: 80.7462 Evaluate side-chains 95 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 617 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9196 Z= 0.244 Angle : 0.584 7.359 12470 Z= 0.309 Chirality : 0.042 0.158 1464 Planarity : 0.004 0.036 1584 Dihedral : 4.744 19.785 1268 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.81 % Allowed : 12.99 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1156 helix: 1.13 (0.19), residues: 760 sheet: -0.10 (0.69), residues: 56 loop : -1.05 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 284 HIS 0.002 0.001 HIS A 211 PHE 0.028 0.002 PHE B 388 TYR 0.010 0.001 TYR B 136 ARG 0.002 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: B 632 LEU cc_start: 0.8445 (mp) cc_final: 0.8186 (mp) REVERT: B 657 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6778 (pm20) REVERT: A 225 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7452 (mtt90) REVERT: A 441 ILE cc_start: 0.9050 (mt) cc_final: 0.8706 (mm) REVERT: A 595 ASP cc_start: 0.7637 (t0) cc_final: 0.7349 (p0) REVERT: A 617 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7583 (tpt) outliers start: 27 outliers final: 12 residues processed: 112 average time/residue: 0.7446 time to fit residues: 93.5590 Evaluate side-chains 106 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9196 Z= 0.400 Angle : 0.634 7.736 12470 Z= 0.335 Chirality : 0.045 0.153 1464 Planarity : 0.004 0.048 1584 Dihedral : 4.749 19.884 1268 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.12 % Allowed : 15.07 % Favored : 81.81 % 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: 0.62 (0.25), residues: 1156 helix: 1.07 (0.18), residues: 760 sheet: 0.16 (0.69), residues: 56 loop : -0.95 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 284 HIS 0.003 0.001 HIS A 211 PHE 0.029 0.002 PHE B 388 TYR 0.013 0.001 TYR B 274 ARG 0.004 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 1.051 Fit side-chains REVERT: B 225 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7555 (mtt90) REVERT: B 468 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7376 (mmmm) REVERT: B 632 LEU cc_start: 0.8395 (mp) cc_final: 0.8075 (mp) REVERT: A 225 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7482 (mtt90) REVERT: A 617 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7669 (tpt) REVERT: A 657 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7135 (pm20) outliers start: 30 outliers final: 17 residues processed: 114 average time/residue: 0.7535 time to fit residues: 95.9402 Evaluate side-chains 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9196 Z= 0.219 Angle : 0.577 8.813 12470 Z= 0.304 Chirality : 0.042 0.190 1464 Planarity : 0.003 0.032 1584 Dihedral : 4.499 17.634 1268 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.39 % Allowed : 17.05 % Favored : 80.56 % 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: 1.08 (0.25), residues: 1156 helix: 1.46 (0.19), residues: 750 sheet: 0.48 (0.87), residues: 36 loop : -0.75 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 284 HIS 0.002 0.001 HIS A 211 PHE 0.025 0.002 PHE B 388 TYR 0.010 0.001 TYR A 232 ARG 0.002 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.997 Fit side-chains REVERT: B 225 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7541 (mtt90) REVERT: B 355 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8000 (t80) REVERT: B 468 LYS cc_start: 0.7615 (mmmm) cc_final: 0.7313 (mmmm) REVERT: B 515 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8237 (ttmm) REVERT: B 632 LEU cc_start: 0.8443 (mp) cc_final: 0.8156 (mp) REVERT: B 657 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: A 355 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7883 (t80) REVERT: A 617 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7628 (tpt) REVERT: A 657 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7057 (pm20) outliers start: 23 outliers final: 10 residues processed: 115 average time/residue: 0.7268 time to fit residues: 93.5062 Evaluate side-chains 109 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9196 Z= 0.240 Angle : 0.577 7.829 12470 Z= 0.301 Chirality : 0.043 0.193 1464 Planarity : 0.003 0.032 1584 Dihedral : 4.376 17.130 1268 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.91 % Allowed : 17.57 % Favored : 79.52 % 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: 1.36 (0.25), residues: 1156 helix: 1.68 (0.19), residues: 740 sheet: 0.55 (0.86), residues: 36 loop : -0.57 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 284 HIS 0.002 0.001 HIS B 211 PHE 0.025 0.002 PHE A 388 TYR 0.010 0.001 TYR A 232 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.991 Fit side-chains REVERT: B 221 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7474 (ttm110) REVERT: B 355 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8002 (t80) REVERT: B 468 LYS cc_start: 0.7642 (mmmm) cc_final: 0.7337 (mmmm) REVERT: B 515 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8216 (ttmm) REVERT: B 632 LEU cc_start: 0.8465 (mp) cc_final: 0.8181 (mp) REVERT: B 657 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: A 221 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7426 (ttm110) REVERT: A 355 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7877 (t80) REVERT: A 617 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7646 (tpt) REVERT: A 657 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7066 (pm20) outliers start: 28 outliers final: 14 residues processed: 119 average time/residue: 0.8010 time to fit residues: 105.7021 Evaluate side-chains 115 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9196 Z= 0.221 Angle : 0.575 7.635 12470 Z= 0.300 Chirality : 0.042 0.183 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.291 17.297 1268 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.95 % Allowed : 17.05 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1156 helix: 1.76 (0.19), residues: 742 sheet: 0.57 (0.85), residues: 36 loop : -0.54 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.002 0.001 HIS A 211 PHE 0.024 0.002 PHE A 388 TYR 0.010 0.001 TYR A 232 ARG 0.002 0.000 ARG B 590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 0.955 Fit side-chains REVERT: B 205 ASN cc_start: 0.8403 (t0) cc_final: 0.8113 (t0) REVERT: B 355 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 468 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7344 (mmmm) REVERT: B 515 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8188 (ttmm) REVERT: B 632 LEU cc_start: 0.8434 (mp) cc_final: 0.8143 (mp) REVERT: B 657 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: A 210 PHE cc_start: 0.8691 (t80) cc_final: 0.8376 (t80) REVERT: A 355 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 404 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7827 (mp) REVERT: A 515 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8345 (ttmm) REVERT: A 617 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7617 (tpt) REVERT: A 657 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7039 (pm20) outliers start: 38 outliers final: 16 residues processed: 120 average time/residue: 0.8287 time to fit residues: 110.0642 Evaluate side-chains 112 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9196 Z= 0.218 Angle : 0.574 7.583 12470 Z= 0.298 Chirality : 0.042 0.175 1464 Planarity : 0.003 0.029 1584 Dihedral : 4.219 16.953 1266 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.12 % Allowed : 18.50 % Favored : 78.38 % 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: 1.57 (0.26), residues: 1156 helix: 1.83 (0.19), residues: 742 sheet: 0.60 (0.86), residues: 36 loop : -0.48 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.002 0.001 HIS A 211 PHE 0.023 0.002 PHE A 388 TYR 0.010 0.001 TYR A 232 ARG 0.007 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.002 Fit side-chains REVERT: B 205 ASN cc_start: 0.8372 (t0) cc_final: 0.8078 (t0) REVERT: B 355 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 468 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7330 (mmmm) REVERT: B 515 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8224 (ttmm) REVERT: B 632 LEU cc_start: 0.8411 (mp) cc_final: 0.8124 (mp) REVERT: B 657 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: A 355 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7900 (t80) REVERT: A 404 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 515 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8300 (ttmm) REVERT: A 617 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7614 (tpt) REVERT: A 657 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7029 (pm20) outliers start: 30 outliers final: 19 residues processed: 119 average time/residue: 0.7165 time to fit residues: 95.5665 Evaluate side-chains 119 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 0.0470 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9196 Z= 0.236 Angle : 0.578 7.692 12470 Z= 0.301 Chirality : 0.043 0.172 1464 Planarity : 0.003 0.031 1584 Dihedral : 4.191 16.640 1266 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.01 % Allowed : 19.33 % Favored : 77.65 % 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: 1.60 (0.26), residues: 1156 helix: 1.87 (0.19), residues: 742 sheet: 0.62 (0.86), residues: 36 loop : -0.48 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.003 0.001 HIS A 211 PHE 0.027 0.002 PHE B 210 TYR 0.010 0.001 TYR A 232 ARG 0.006 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: B 355 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8031 (t80) REVERT: B 468 LYS cc_start: 0.7653 (mmmm) cc_final: 0.7333 (mmmm) REVERT: B 515 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8205 (ttmm) REVERT: B 632 LEU cc_start: 0.8413 (mp) cc_final: 0.8116 (mp) REVERT: B 657 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: A 355 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 404 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7832 (mp) REVERT: A 515 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8301 (ttmm) REVERT: A 657 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7104 (pm20) outliers start: 29 outliers final: 19 residues processed: 117 average time/residue: 0.7254 time to fit residues: 94.8557 Evaluate side-chains 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9196 Z= 0.210 Angle : 0.567 7.580 12470 Z= 0.296 Chirality : 0.042 0.173 1464 Planarity : 0.003 0.033 1584 Dihedral : 4.134 16.780 1266 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 19.96 % Favored : 77.55 % 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: 1.73 (0.26), residues: 1156 helix: 1.96 (0.19), residues: 742 sheet: 0.73 (0.86), residues: 36 loop : -0.43 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 284 HIS 0.003 0.000 HIS B 211 PHE 0.023 0.002 PHE A 388 TYR 0.010 0.001 TYR A 232 ARG 0.006 0.000 ARG B 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.876 Fit side-chains REVERT: B 355 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 468 LYS cc_start: 0.7629 (mmmm) cc_final: 0.7318 (mmmm) REVERT: B 515 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8222 (ttmm) REVERT: B 632 LEU cc_start: 0.8430 (mp) cc_final: 0.8144 (mp) REVERT: A 355 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7898 (t80) REVERT: A 404 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 515 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8291 (ttmm) outliers start: 24 outliers final: 19 residues processed: 110 average time/residue: 0.7132 time to fit residues: 88.0200 Evaluate side-chains 112 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.208869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121656 restraints weight = 9613.232| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.03 r_work: 0.3301 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9196 Z= 0.201 Angle : 0.562 7.513 12470 Z= 0.290 Chirality : 0.041 0.169 1464 Planarity : 0.003 0.033 1584 Dihedral : 4.135 17.627 1266 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 20.58 % Favored : 77.13 % 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: 1.79 (0.26), residues: 1156 helix: 2.01 (0.19), residues: 742 sheet: 0.77 (0.86), residues: 36 loop : -0.43 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 284 HIS 0.003 0.000 HIS A 211 PHE 0.024 0.002 PHE B 210 TYR 0.010 0.001 TYR A 232 ARG 0.006 0.000 ARG B 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.17 seconds wall clock time: 49 minutes 48.83 seconds (2988.83 seconds total)