Starting phenix.real_space_refine on Thu Mar 14 13:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/03_2024/7pro_13609.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/03_2024/7pro_13609.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/7pro_13609/03_2024/7pro_13609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/03_2024/7pro_13609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/03_2024/7pro_13609.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/03_2024/7pro_13609.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= -0.000 sd= 0.152 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 "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 PHE 210": "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 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" 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 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 ARG 570": "NH1" <-> "NH2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" 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 PHE 210": "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 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 403": "OE1" <-> "OE2" 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 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 ARG 570": "NH1" <-> "NH2" Residue "B ASP 645": "OD1" <-> "OD2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9032 Number of models: 1 Model: "" Number of chains: 2 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} 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} Time building chain proxies: 5.22, per 1000 atoms: 0.58 Number of scatterers: 9032 At special positions: 0 Unit cell: (117.312, 85.696, 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: 2.97 Conformation dependent library (CDL) restraints added in 1.6 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: 44 helices and 4 sheets defined 67.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.083A pdb=" N GLN A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 144 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 159 through 205 removed outlier: 3.538A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.765A 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: 3.721A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.530A pdb=" N SER A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.752A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 396 through 417 removed outlier: 4.723A pdb=" N TYR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 4.565A 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 530 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 569 removed outlier: 4.162A pdb=" N GLN A 568 " --> pdb=" O HIS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 609 through 625 Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.186A pdb=" N GLU A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 109 through 144 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 159 through 205 removed outlier: 3.539A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.764A 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: 3.721A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.529A pdb=" N SER B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.753A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 417 removed outlier: 4.724A pdb=" N TYR B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 removed outlier: 4.565A 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 530 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 569 removed outlier: 4.161A pdb=" N GLN B 568 " --> pdb=" O HIS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 609 through 625 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 670 through 674 removed outlier: 4.187A pdb=" N GLU B 673 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 464 removed outlier: 4.660A pdb=" N VAL A 446 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER A 461 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU A 444 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 463 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A 442 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 446 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN A 495 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.566A pdb=" N GLY A 518 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A 469 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE A 648 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA A 471 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU A 650 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 473 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU A 657 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 457 through 464 removed outlier: 4.660A pdb=" N VAL B 446 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER B 461 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU B 444 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 463 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 442 " --> pdb=" O THR B 463 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 446 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN B 495 " --> pdb=" O VAL B 446 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 517 through 519 removed outlier: 6.566A pdb=" N GLY B 518 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS B 469 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 648 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA B 471 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 650 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 473 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 657 " --> pdb=" O VAL B 649 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1782 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: 2.68 Time building geometry restraints manager: 3.25 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: 2519 1.33 - 1.45: 1459 1.45 - 1.57: 5174 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 9196 Sorted by residual: bond pdb=" CG LEU B 390 " pdb=" CD1 LEU B 390 " ideal model delta sigma weight residual 1.521 1.398 0.123 3.30e-02 9.18e+02 1.39e+01 bond pdb=" CG LEU A 390 " pdb=" CD1 LEU A 390 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.38e+01 bond pdb=" C SER B 156 " pdb=" N ALA B 157 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.40e-02 5.10e+03 6.63e+00 bond pdb=" C SER A 156 " pdb=" N ALA A 157 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.40e-02 5.10e+03 6.38e+00 bond pdb=" CB ARG A 170 " pdb=" CG ARG A 170 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 5.04e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 94.75 - 102.65: 38 102.65 - 110.55: 2681 110.55 - 118.45: 4537 118.45 - 126.35: 5112 126.35 - 134.24: 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 113.60 122.96 -9.36 1.90e+00 2.77e-01 2.43e+01 angle pdb=" CA TRP B 284 " pdb=" CB TRP B 284 " pdb=" CG TRP B 284 " ideal model delta sigma weight residual 113.60 122.95 -9.35 1.90e+00 2.77e-01 2.42e+01 angle pdb=" C LYS B 625 " pdb=" N GLU B 626 " pdb=" CA GLU B 626 " ideal model delta sigma weight residual 122.40 129.10 -6.70 1.45e+00 4.76e-01 2.13e+01 angle pdb=" C LYS A 625 " pdb=" N GLU A 626 " pdb=" CA GLU A 626 " ideal model delta sigma weight residual 122.40 129.10 -6.70 1.45e+00 4.76e-01 2.13e+01 angle pdb=" CA LEU A 586 " pdb=" CB LEU A 586 " pdb=" CG LEU A 586 " ideal model delta sigma weight residual 116.30 132.30 -16.00 3.50e+00 8.16e-02 2.09e+01 ... (remaining 12465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5041 17.79 - 35.58: 383 35.58 - 53.36: 70 53.36 - 71.15: 10 71.15 - 88.94: 12 Dihedral angle restraints: 5516 sinusoidal: 2156 harmonic: 3360 Sorted by residual: dihedral pdb=" CA MET A 665 " pdb=" C MET A 665 " pdb=" N GLU A 666 " pdb=" CA GLU A 666 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA MET B 665 " pdb=" C MET B 665 " pdb=" N GLU B 666 " pdb=" CA GLU B 666 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA SER B 156 " pdb=" C SER B 156 " pdb=" N ALA B 157 " pdb=" CA ALA B 157 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 887 0.052 - 0.105: 448 0.105 - 0.157: 106 0.157 - 0.209: 20 0.209 - 0.261: 3 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CB VAL A 155 " pdb=" CA VAL A 155 " pdb=" CG1 VAL A 155 " pdb=" CG2 VAL A 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL B 155 " pdb=" CA VAL B 155 " pdb=" CG1 VAL B 155 " pdb=" CG2 VAL B 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASP B 108 " pdb=" N ASP B 108 " pdb=" C ASP B 108 " pdb=" CB ASP B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1461 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 405 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C ARG B 405 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG B 405 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN B 406 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 405 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ARG A 405 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG A 405 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 406 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 138 " 0.091 9.50e-02 1.11e+02 4.60e-02 6.54e+00 pdb=" NE ARG B 138 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 138 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG B 138 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 138 " 0.017 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1020 2.73 - 3.28: 9288 3.28 - 3.82: 15229 3.82 - 4.36: 18021 4.36 - 4.90: 31384 Nonbonded interactions: 74942 Sorted by model distance: nonbonded pdb=" OH TYR A 537 " pdb=" OE2 GLU B 322 " model vdw 2.192 2.440 nonbonded pdb=" OE2 GLU A 322 " pdb=" OH TYR B 537 " model vdw 2.204 2.440 nonbonded pdb=" O GLY B 566 " pdb=" OG1 THR B 569 " model vdw 2.211 2.440 nonbonded pdb=" O GLY A 566 " pdb=" OG1 THR A 569 " model vdw 2.211 2.440 nonbonded pdb=" O LEU B 586 " pdb=" OG SER B 589 " model vdw 2.342 2.440 ... (remaining 74937 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: 1.640 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: 7.320 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.240 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.123 9196 Z= 0.771 Angle : 1.092 15.996 12470 Z= 0.610 Chirality : 0.062 0.261 1464 Planarity : 0.009 0.052 1584 Dihedral : 13.800 88.940 3352 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.65 (0.23), residues: 1156 helix: -0.49 (0.17), residues: 754 sheet: -1.95 (0.58), residues: 58 loop : -2.05 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 284 HIS 0.010 0.002 HIS B 132 PHE 0.040 0.004 PHE B 137 TYR 0.044 0.004 TYR B 315 ARG 0.041 0.006 ARG B 138 *********************** 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 119 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 516 SER cc_start: 0.7648 (m) cc_final: 0.7418 (m) REVERT: A 568 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8127 (mp10) REVERT: A 585 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6480 (tpp80) REVERT: A 617 MET cc_start: 0.7925 (tpt) cc_final: 0.7575 (tpp) REVERT: B 400 VAL cc_start: 0.8584 (t) cc_final: 0.8348 (p) REVERT: B 516 SER cc_start: 0.7892 (m) cc_final: 0.7328 (p) REVERT: B 645 ASP cc_start: 0.7077 (t0) cc_final: 0.6851 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.9845 time to fit residues: 126.9081 Evaluate side-chains 93 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 317 ASN A 384 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 317 ASN B 384 ASN B 495 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1278 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= 0.204 Angle : 0.618 7.267 12470 Z= 0.325 Chirality : 0.042 0.130 1464 Planarity : 0.004 0.033 1584 Dihedral : 4.919 20.173 1266 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.87 % Allowed : 8.94 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1156 helix: 0.83 (0.18), residues: 744 sheet: -1.90 (0.56), residues: 56 loop : -1.67 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 284 HIS 0.004 0.001 HIS A 555 PHE 0.020 0.002 PHE A 388 TYR 0.022 0.002 TYR B 315 ARG 0.004 0.001 ARG A 536 *********************** 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 119 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.008 Fit side-chains REVERT: A 311 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: A 405 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7515 (mmt-90) REVERT: A 585 ARG cc_start: 0.6642 (mtt-85) cc_final: 0.6440 (tpp80) REVERT: B 301 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7576 (m) REVERT: B 424 ILE cc_start: 0.8028 (mm) cc_final: 0.7663 (mp) REVERT: B 516 SER cc_start: 0.8058 (m) cc_final: 0.7615 (p) REVERT: B 632 LEU cc_start: 0.7090 (mt) cc_final: 0.6781 (tp) REVERT: B 645 ASP cc_start: 0.6793 (t0) cc_final: 0.6521 (t0) outliers start: 18 outliers final: 7 residues processed: 111 average time/residue: 0.7998 time to fit residues: 98.5291 Evaluate side-chains 98 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 519 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 568 GLN B 205 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1548 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= 0.241 Angle : 0.587 6.721 12470 Z= 0.309 Chirality : 0.042 0.130 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.674 19.228 1266 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.39 % Allowed : 13.51 % Favored : 84.10 % 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: 0.47 (0.25), residues: 1156 helix: 1.32 (0.18), residues: 744 sheet: -1.92 (0.53), residues: 56 loop : -1.45 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 284 HIS 0.003 0.001 HIS B 661 PHE 0.021 0.002 PHE B 388 TYR 0.018 0.002 TYR B 315 ARG 0.004 0.000 ARG A 536 *********************** 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 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: A 492 ASP cc_start: 0.7348 (m-30) cc_final: 0.7084 (m-30) REVERT: B 301 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7497 (m) REVERT: B 516 SER cc_start: 0.7977 (m) cc_final: 0.7478 (p) REVERT: B 568 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7967 (mp10) REVERT: B 632 LEU cc_start: 0.7170 (mt) cc_final: 0.6800 (tp) REVERT: B 645 ASP cc_start: 0.6829 (t0) cc_final: 0.6550 (t0) outliers start: 23 outliers final: 9 residues processed: 102 average time/residue: 0.8714 time to fit residues: 98.0019 Evaluate side-chains 97 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 519 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 0.2980 chunk 100 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 205 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9196 Z= 0.374 Angle : 0.639 7.618 12470 Z= 0.335 Chirality : 0.045 0.134 1464 Planarity : 0.004 0.039 1584 Dihedral : 4.717 21.052 1266 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.49 % Allowed : 16.63 % Favored : 80.87 % 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: 0.50 (0.25), residues: 1156 helix: 1.26 (0.18), residues: 744 sheet: -1.60 (0.54), residues: 58 loop : -1.28 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 284 HIS 0.004 0.001 HIS B 132 PHE 0.022 0.002 PHE A 388 TYR 0.016 0.002 TYR A 567 ARG 0.003 0.001 ARG A 570 *********************** 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 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 492 ASP cc_start: 0.7364 (m-30) cc_final: 0.7102 (m-30) REVERT: A 516 SER cc_start: 0.7550 (OUTLIER) cc_final: 0.7147 (p) REVERT: B 516 SER cc_start: 0.7962 (m) cc_final: 0.7452 (p) REVERT: B 568 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7999 (mp10) outliers start: 24 outliers final: 15 residues processed: 103 average time/residue: 0.9269 time to fit residues: 104.7064 Evaluate side-chains 105 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 519 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.0770 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 418 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 205 ASN B 495 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9196 Z= 0.187 Angle : 0.555 7.115 12470 Z= 0.290 Chirality : 0.040 0.128 1464 Planarity : 0.003 0.031 1584 Dihedral : 4.464 21.282 1266 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.12 % Allowed : 16.74 % Favored : 80.15 % 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: 0.98 (0.25), residues: 1156 helix: 1.67 (0.19), residues: 744 sheet: -1.56 (0.57), residues: 56 loop : -1.17 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 284 HIS 0.003 0.001 HIS B 661 PHE 0.021 0.002 PHE A 388 TYR 0.015 0.001 TYR A 567 ARG 0.003 0.000 ARG A 570 *********************** 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 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7571 (m) REVERT: A 311 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: A 492 ASP cc_start: 0.7311 (m-30) cc_final: 0.7027 (m-30) REVERT: A 516 SER cc_start: 0.7595 (OUTLIER) cc_final: 0.7197 (p) REVERT: B 301 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7541 (m) REVERT: B 516 SER cc_start: 0.7965 (m) cc_final: 0.7461 (p) REVERT: B 568 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7949 (mp10) outliers start: 30 outliers final: 14 residues processed: 116 average time/residue: 0.8364 time to fit residues: 106.9522 Evaluate side-chains 106 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 609 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 418 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 205 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2083 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= 0.224 Angle : 0.569 7.684 12470 Z= 0.296 Chirality : 0.041 0.131 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.393 20.938 1266 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.81 % Allowed : 17.67 % 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: 1.19 (0.25), residues: 1156 helix: 1.78 (0.18), residues: 746 sheet: -1.16 (0.61), residues: 58 loop : -1.02 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 284 HIS 0.003 0.001 HIS B 661 PHE 0.019 0.002 PHE A 388 TYR 0.014 0.001 TYR A 567 ARG 0.004 0.000 ARG A 570 *********************** 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 117 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7549 (m) REVERT: A 311 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 492 ASP cc_start: 0.7365 (m-30) cc_final: 0.7063 (m-30) REVERT: A 516 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.7220 (p) REVERT: B 301 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7508 (m) REVERT: B 516 SER cc_start: 0.7952 (m) cc_final: 0.7453 (p) REVERT: B 568 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7966 (mp10) outliers start: 27 outliers final: 14 residues processed: 111 average time/residue: 0.8253 time to fit residues: 101.0581 Evaluate side-chains 107 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 69 optimal weight: 0.0050 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9196 Z= 0.175 Angle : 0.547 10.414 12470 Z= 0.282 Chirality : 0.040 0.127 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.236 20.061 1266 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.22 % Allowed : 17.15 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1156 helix: 2.01 (0.19), residues: 744 sheet: -1.21 (0.63), residues: 56 loop : -0.95 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 284 HIS 0.003 0.001 HIS B 661 PHE 0.019 0.001 PHE A 388 TYR 0.014 0.001 TYR A 567 ARG 0.004 0.000 ARG A 570 *********************** 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: 31 poor density : 92 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7488 (m) REVERT: A 311 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: A 516 SER cc_start: 0.7691 (OUTLIER) cc_final: 0.7318 (p) REVERT: B 262 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 271 MET cc_start: 0.8382 (mmm) cc_final: 0.8059 (mmm) REVERT: B 301 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7455 (m) REVERT: B 516 SER cc_start: 0.7959 (m) cc_final: 0.7463 (p) REVERT: B 568 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7932 (mp10) outliers start: 31 outliers final: 13 residues processed: 116 average time/residue: 0.8608 time to fit residues: 109.6334 Evaluate side-chains 108 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 418 GLN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 205 ASN B 418 GLN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9196 Z= 0.351 Angle : 0.624 7.660 12470 Z= 0.326 Chirality : 0.044 0.137 1464 Planarity : 0.004 0.034 1584 Dihedral : 4.431 20.250 1266 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.60 % Allowed : 18.40 % 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: 1.14 (0.25), residues: 1156 helix: 1.68 (0.18), residues: 746 sheet: -1.36 (0.62), residues: 60 loop : -0.84 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 284 HIS 0.003 0.001 HIS B 661 PHE 0.018 0.002 PHE B 355 TYR 0.015 0.002 TYR B 232 ARG 0.004 0.000 ARG B 570 *********************** 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 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: A 513 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7299 (tp) REVERT: A 516 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7291 (p) REVERT: B 262 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: B 516 SER cc_start: 0.7931 (m) cc_final: 0.7423 (p) REVERT: B 568 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7995 (mp10) outliers start: 25 outliers final: 15 residues processed: 108 average time/residue: 0.8966 time to fit residues: 106.2306 Evaluate side-chains 101 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 205 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.197 Angle : 0.562 6.943 12470 Z= 0.292 Chirality : 0.041 0.126 1464 Planarity : 0.003 0.032 1584 Dihedral : 4.258 19.920 1266 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.60 % Allowed : 18.61 % Favored : 78.79 % 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: 1.41 (0.25), residues: 1156 helix: 1.93 (0.19), residues: 746 sheet: -1.24 (0.64), residues: 60 loop : -0.83 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 284 HIS 0.004 0.001 HIS B 661 PHE 0.019 0.002 PHE A 388 TYR 0.014 0.001 TYR A 567 ARG 0.004 0.000 ARG B 570 *********************** 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 111 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.8449 (mmm) cc_final: 0.8139 (mmm) REVERT: A 301 THR cc_start: 0.7981 (t) cc_final: 0.7501 (m) REVERT: A 311 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: A 516 SER cc_start: 0.7679 (OUTLIER) cc_final: 0.7333 (p) REVERT: B 262 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: B 271 MET cc_start: 0.8444 (mmm) cc_final: 0.8063 (mmm) REVERT: B 301 THR cc_start: 0.7977 (t) cc_final: 0.7494 (m) REVERT: B 516 SER cc_start: 0.7923 (m) cc_final: 0.7433 (p) REVERT: B 568 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7945 (mp10) REVERT: B 577 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5757 (mmt) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 0.9056 time to fit residues: 105.2495 Evaluate side-chains 106 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 106 optimal weight: 0.0870 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 205 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9196 Z= 0.207 Angle : 0.560 7.166 12470 Z= 0.293 Chirality : 0.041 0.128 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.199 19.349 1266 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 18.71 % Favored : 78.79 % 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: 1.50 (0.25), residues: 1156 helix: 1.99 (0.19), residues: 746 sheet: -1.13 (0.64), residues: 60 loop : -0.80 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 284 HIS 0.004 0.001 HIS B 661 PHE 0.018 0.001 PHE A 388 TYR 0.013 0.001 TYR A 567 ARG 0.004 0.000 ARG A 570 ********************** 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 114 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 THR cc_start: 0.7943 (t) cc_final: 0.7462 (m) REVERT: A 311 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: A 516 SER cc_start: 0.7642 (OUTLIER) cc_final: 0.7286 (p) REVERT: B 262 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: B 301 THR cc_start: 0.7942 (t) cc_final: 0.7464 (m) REVERT: B 513 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7086 (tp) REVERT: B 516 SER cc_start: 0.7896 (m) cc_final: 0.7387 (p) REVERT: B 568 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7958 (mp10) REVERT: B 600 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.5932 (m-80) outliers start: 24 outliers final: 15 residues processed: 109 average time/residue: 0.8771 time to fit residues: 104.9278 Evaluate side-chains 109 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 205 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.219349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146223 restraints weight = 9477.334| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.83 r_work: 0.3642 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9196 Z= 0.168 Angle : 0.538 6.582 12470 Z= 0.280 Chirality : 0.039 0.127 1464 Planarity : 0.003 0.029 1584 Dihedral : 4.091 18.753 1266 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.18 % Allowed : 19.23 % Favored : 78.59 % 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: 1.69 (0.25), residues: 1156 helix: 2.15 (0.19), residues: 746 sheet: -1.00 (0.66), residues: 60 loop : -0.76 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 284 HIS 0.004 0.001 HIS B 661 PHE 0.018 0.001 PHE B 388 TYR 0.014 0.001 TYR A 567 ARG 0.004 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.79 seconds wall clock time: 50 minutes 41.79 seconds (3041.79 seconds total)