Starting phenix.real_space_refine on Tue Nov 14 16:30:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/11_2023/7psd_13612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/11_2023/7psd_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_13612/11_2023/7psd_13612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/11_2023/7psd_13612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/11_2023/7psd_13612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psd_13612/11_2023/7psd_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 5.27, per 1000 atoms: 0.58 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: 3.73 Conformation dependent library (CDL) restraints added in 1.8 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: 0.94 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: 3.08 Time building geometry restraints manager: 4.01 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.190 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.280 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.520 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.023 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 123 average time/residue: 0.8148 time to fit residues: 110.9165 Evaluate side-chains 103 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1260 time to fit residues: 1.6240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 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: 0.8193 moved from start: 0.1307 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= 0.249 Angle : 0.630 7.316 12470 Z= 0.335 Chirality : 0.043 0.168 1464 Planarity : 0.004 0.045 1584 Dihedral : 5.138 22.141 1266 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.66 % Allowed : 9.88 % Favored : 88.46 % 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: 0.07 (0.25), residues: 1156 helix: 0.64 (0.18), residues: 754 sheet: -0.39 (0.68), residues: 56 loop : -1.03 (0.37), residues: 346 *********************** 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 116 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.991 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 0.6786 time to fit residues: 83.6936 Evaluate side-chains 96 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 4 average time/residue: 0.1818 time to fit residues: 2.4644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 87 optimal weight: 0.0000 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9196 Z= 0.210 Angle : 0.582 7.514 12470 Z= 0.307 Chirality : 0.042 0.182 1464 Planarity : 0.003 0.034 1584 Dihedral : 4.704 19.804 1266 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.39 % Allowed : 14.03 % Favored : 83.58 % 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: 0.67 (0.25), residues: 1156 helix: 1.18 (0.19), residues: 760 sheet: -0.13 (0.68), residues: 56 loop : -1.05 (0.36), residues: 340 *********************** 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 115 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.018 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 108 average time/residue: 0.7731 time to fit residues: 93.2384 Evaluate side-chains 97 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 5 average time/residue: 0.3607 time to fit residues: 3.5495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8297 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 9196 Z= 0.591 Angle : 0.723 7.609 12470 Z= 0.383 Chirality : 0.051 0.176 1464 Planarity : 0.005 0.064 1584 Dihedral : 4.907 17.946 1266 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.53 % Allowed : 15.38 % Favored : 81.08 % 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: 0.34 (0.25), residues: 1156 helix: 0.83 (0.18), residues: 756 sheet: 0.10 (0.68), residues: 56 loop : -0.96 (0.36), residues: 344 *********************** 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 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 121 average time/residue: 0.7897 time to fit residues: 106.3819 Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 9 average time/residue: 0.5379 time to fit residues: 6.9260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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: 0.8208 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9196 Z= 0.244 Angle : 0.588 7.528 12470 Z= 0.310 Chirality : 0.043 0.165 1464 Planarity : 0.004 0.035 1584 Dihedral : 4.619 17.602 1266 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.01 % Allowed : 16.63 % Favored : 80.35 % 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: 0.77 (0.25), residues: 1156 helix: 1.20 (0.19), residues: 760 sheet: 0.25 (0.68), residues: 56 loop : -0.91 (0.36), residues: 340 *********************** 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 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.925 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 120 average time/residue: 0.7080 time to fit residues: 95.5889 Evaluate side-chains 106 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 5 average time/residue: 0.3212 time to fit residues: 3.4354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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: 0.8232 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9196 Z= 0.323 Angle : 0.613 7.439 12470 Z= 0.323 Chirality : 0.045 0.157 1464 Planarity : 0.004 0.039 1584 Dihedral : 4.548 16.656 1266 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.33 % Allowed : 17.57 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1156 helix: 1.23 (0.19), residues: 760 sheet: 0.45 (0.70), residues: 56 loop : -0.88 (0.36), residues: 340 *********************** 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 129 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.019 Fit side-chains outliers start: 32 outliers final: 13 residues processed: 118 average time/residue: 0.7270 time to fit residues: 96.1897 Evaluate side-chains 108 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 4 average time/residue: 0.1706 time to fit residues: 2.4305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** B 621 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: 0.8190 moved from start: 0.2345 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= 0.229 Angle : 0.578 7.445 12470 Z= 0.302 Chirality : 0.043 0.179 1464 Planarity : 0.003 0.027 1584 Dihedral : 4.363 16.179 1266 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.49 % Allowed : 19.23 % Favored : 78.27 % 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: 1.34 (0.25), residues: 1156 helix: 1.66 (0.19), residues: 740 sheet: 0.62 (0.71), residues: 56 loop : -0.65 (0.36), residues: 360 *********************** 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 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.951 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 118 average time/residue: 0.6756 time to fit residues: 90.7373 Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 5 average time/residue: 0.1545 time to fit residues: 2.5944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9196 Z= 0.209 Angle : 0.579 7.600 12470 Z= 0.299 Chirality : 0.042 0.181 1464 Planarity : 0.003 0.027 1584 Dihedral : 4.260 15.926 1266 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.12 % Allowed : 19.85 % Favored : 77.03 % 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: 1.84 (0.19), residues: 742 sheet: 0.86 (0.73), residues: 56 loop : -0.60 (0.37), residues: 358 *********************** 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 : 1.037 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 125 average time/residue: 0.6521 time to fit residues: 92.2582 Evaluate side-chains 110 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 3 average time/residue: 0.1503 time to fit residues: 1.9730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9196 Z= 0.238 Angle : 0.585 8.192 12470 Z= 0.304 Chirality : 0.043 0.172 1464 Planarity : 0.003 0.029 1584 Dihedral : 4.243 15.891 1266 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.49 % Allowed : 20.79 % Favored : 76.72 % 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: 1.62 (0.26), residues: 1156 helix: 1.87 (0.19), residues: 742 sheet: 0.69 (0.69), residues: 66 loop : -0.56 (0.37), residues: 348 *********************** 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 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.080 Fit side-chains outliers start: 24 outliers final: 22 residues processed: 114 average time/residue: 0.7482 time to fit residues: 95.6762 Evaluate side-chains 114 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 6 average time/residue: 0.4564 time to fit residues: 4.6349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9196 Z= 0.196 Angle : 0.578 8.017 12470 Z= 0.299 Chirality : 0.042 0.176 1464 Planarity : 0.003 0.033 1584 Dihedral : 4.170 16.405 1266 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.08 % Allowed : 21.41 % Favored : 76.51 % 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: 1.83 (0.26), residues: 1156 helix: 2.02 (0.19), residues: 742 sheet: 0.93 (0.69), residues: 66 loop : -0.47 (0.38), residues: 348 ********************** 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 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.074 Fit side-chains outliers start: 20 outliers final: 20 residues processed: 110 average time/residue: 0.6667 time to fit residues: 83.2935 Evaluate side-chains 112 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 5 average time/residue: 0.1027 time to fit residues: 2.1473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.0060 chunk 38 optimal weight: 0.0270 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN A 429 ASN A 503 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.210582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124945 restraints weight = 9591.291| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.01 r_work: 0.3350 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9196 Z= 0.164 Angle : 0.552 8.011 12470 Z= 0.282 Chirality : 0.041 0.166 1464 Planarity : 0.003 0.036 1584 Dihedral : 4.064 15.339 1266 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.77 % Allowed : 21.83 % Favored : 76.40 % 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: 1.98 (0.26), residues: 1156 helix: 2.17 (0.19), residues: 742 sheet: 0.85 (0.82), residues: 46 loop : -0.41 (0.36), residues: 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2707.66 seconds wall clock time: 49 minutes 15.83 seconds (2955.83 seconds total)