Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 15:53:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/04_2023/8eob_28333_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/04_2023/8eob_28333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/04_2023/8eob_28333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/04_2023/8eob_28333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/04_2023/8eob_28333_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/04_2023/8eob_28333_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.969 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 6411 2.51 5 N 1701 2.21 5 O 1975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5053 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 17, 'TRANS': 606} Chain breaks: 2 Chain: "B" Number of atoms: 5024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5024 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 17, 'TRANS': 603} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.65, per 1000 atoms: 0.56 Number of scatterers: 10141 At special positions: 0 Unit cell: (94.696, 94.696, 130.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1975 8.00 N 1701 7.00 C 6411 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: 4.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 9 sheets defined 40.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 36 through 59 removed outlier: 3.716A pdb=" N PHE A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 44 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 398 through 421 removed outlier: 4.035A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 443 removed outlier: 6.505A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.541A pdb=" N LYS A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.552A pdb=" N GLN A 524 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.517A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 619' Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 36 through 59 removed outlier: 3.826A pdb=" N PHE B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 40 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 44 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 398 through 421 removed outlier: 4.148A pdb=" N GLU B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 443 removed outlier: 6.411A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 4.236A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.030A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 503 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 4.133A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 570 removed outlier: 5.482A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 617 through 620 No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 633 through 644 Processing helix chain 'B' and resid 649 through 666 Processing helix chain 'B' and resid 673 through 688 Processing sheet with id= A, first strand: chain 'A' and resid 212 through 216 removed outlier: 3.712A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 217 through 219 Processing sheet with id= C, first strand: chain 'A' and resid 360 through 364 removed outlier: 6.879A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP A 364 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 353 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS A 354 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 532 through 535 Processing sheet with id= E, first strand: chain 'A' and resid 577 through 580 Processing sheet with id= F, first strand: chain 'B' and resid 165 through 169 removed outlier: 6.780A pdb=" N HIS B 184 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 143 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 182 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 145 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 147 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 178 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE B 75 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 214 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR B 216 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 361 through 364 removed outlier: 7.048A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LYS B 354 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 379 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR B 356 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 381 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 532 through 535 Processing sheet with id= I, first strand: chain 'B' and resid 577 through 580 416 hydrogen bonds defined for protein. 1062 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: 3.10 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3319 1.34 - 1.46: 2159 1.46 - 1.58: 4746 1.58 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 10309 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.566 0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 10304 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.90: 177 105.90 - 112.94: 5659 112.94 - 119.98: 3495 119.98 - 127.01: 4464 127.01 - 134.05: 82 Bond angle restraints: 13877 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.14 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 111.34 15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.37 10.71 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " pdb=" O2G ANP A 801 " ideal model delta sigma weight residual 101.05 110.02 -8.97 3.00e+00 1.11e-01 8.94e+00 ... (remaining 13872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5943 17.72 - 35.44: 326 35.44 - 53.15: 56 53.15 - 70.87: 6 70.87 - 88.59: 2 Dihedral angle restraints: 6333 sinusoidal: 2672 harmonic: 3661 Sorted by residual: dihedral pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" CB LYS B 481 " pdb=" CG LYS B 481 " ideal model delta sinusoidal sigma weight residual -180.00 -125.36 -54.64 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" N ASN B 150 " pdb=" CA ASN B 150 " pdb=" CB ASN B 150 " pdb=" CG ASN B 150 " ideal model delta sinusoidal sigma weight residual -60.00 -113.44 53.44 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA GLU A 368 " pdb=" CB GLU A 368 " pdb=" CG GLU A 368 " pdb=" CD GLU A 368 " ideal model delta sinusoidal sigma weight residual 60.00 111.90 -51.90 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 6330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1288 0.052 - 0.104: 213 0.104 - 0.156: 42 0.156 - 0.208: 0 0.208 - 0.260: 2 Chirality restraints: 1545 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE B 335 " pdb=" N ILE B 335 " pdb=" C ILE B 335 " pdb=" CB ILE B 335 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1542 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 371 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 371 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 52 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ASP A 52 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP A 52 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 53 " -0.009 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 86 2.54 - 3.13: 7983 3.13 - 3.72: 15517 3.72 - 4.31: 21941 4.31 - 4.90: 37210 Nonbonded interactions: 82737 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb=" O2G ANP B 801 " model vdw 1.945 3.040 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 1.979 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 1.988 2.170 nonbonded pdb=" N3B ANP A 801 " pdb="MG MG A 802 " model vdw 2.062 2.250 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 802 " model vdw 2.081 2.170 ... (remaining 82732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 220 or resid 275 through 345 or resid 351 throu \ gh 690 or resid 801 through 802)) 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.760 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.340 Find NCS groups from input model: 0.570 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.152 10309 Z= 0.294 Angle : 0.607 16.814 13877 Z= 0.296 Chirality : 0.041 0.260 1545 Planarity : 0.003 0.043 1765 Dihedral : 11.238 88.591 3959 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.78 % 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: 0.42 (0.24), residues: 1233 helix: 1.34 (0.24), residues: 509 sheet: 0.36 (0.35), residues: 227 loop : -0.83 (0.27), residues: 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 182 average time/residue: 0.2522 time to fit residues: 63.2567 Evaluate side-chains 113 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0896 time to fit residues: 2.9662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 676 HIS A 678 ASN B 80 GLN B 389 ASN B 493 GLN B 674 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 10309 Z= 0.218 Angle : 0.463 5.345 13877 Z= 0.244 Chirality : 0.040 0.141 1545 Planarity : 0.003 0.040 1765 Dihedral : 4.941 58.578 1356 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.87 % 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: 0.70 (0.24), residues: 1233 helix: 1.51 (0.24), residues: 494 sheet: 0.54 (0.35), residues: 229 loop : -0.58 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 125 average time/residue: 0.2203 time to fit residues: 40.3391 Evaluate side-chains 105 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0970 time to fit residues: 3.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.0040 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 10309 Z= 0.217 Angle : 0.453 5.461 13877 Z= 0.239 Chirality : 0.040 0.144 1545 Planarity : 0.003 0.040 1765 Dihedral : 4.766 51.069 1356 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.60 % 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: 0.64 (0.24), residues: 1233 helix: 1.41 (0.24), residues: 503 sheet: 0.56 (0.36), residues: 224 loop : -0.59 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 114 average time/residue: 0.2217 time to fit residues: 37.3881 Evaluate side-chains 95 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0959 time to fit residues: 2.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10309 Z= 0.121 Angle : 0.411 5.608 13877 Z= 0.218 Chirality : 0.038 0.136 1545 Planarity : 0.003 0.041 1765 Dihedral : 4.423 44.822 1356 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.25 % 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: 0.68 (0.25), residues: 1233 helix: 1.40 (0.24), residues: 509 sheet: 0.62 (0.36), residues: 225 loop : -0.57 (0.28), residues: 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 123 average time/residue: 0.2295 time to fit residues: 41.1566 Evaluate side-chains 105 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1024 time to fit residues: 2.9427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0570 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10309 Z= 0.116 Angle : 0.415 6.513 13877 Z= 0.217 Chirality : 0.038 0.131 1545 Planarity : 0.003 0.041 1765 Dihedral : 4.255 40.595 1356 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.80 % 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: 0.71 (0.25), residues: 1233 helix: 1.41 (0.24), residues: 507 sheet: 0.73 (0.36), residues: 224 loop : -0.57 (0.28), residues: 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.2180 time to fit residues: 36.2724 Evaluate side-chains 102 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0948 time to fit residues: 2.3836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 119 optimal weight: 20.0000 chunk 99 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN B 389 ASN B 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 10309 Z= 0.241 Angle : 0.467 5.690 13877 Z= 0.242 Chirality : 0.040 0.143 1545 Planarity : 0.003 0.042 1765 Dihedral : 4.563 48.722 1356 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.53 % 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: 0.76 (0.25), residues: 1233 helix: 1.48 (0.24), residues: 491 sheet: 0.66 (0.36), residues: 227 loop : -0.46 (0.28), residues: 515 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 0.2135 time to fit residues: 29.2998 Evaluate side-chains 92 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0960 time to fit residues: 2.3283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 10309 Z= 0.155 Angle : 0.432 6.964 13877 Z= 0.225 Chirality : 0.038 0.137 1545 Planarity : 0.003 0.041 1765 Dihedral : 4.405 45.473 1356 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.45 % 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: 0.75 (0.25), residues: 1233 helix: 1.44 (0.24), residues: 502 sheet: 0.78 (0.36), residues: 225 loop : -0.55 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 100 average time/residue: 0.2201 time to fit residues: 32.6121 Evaluate side-chains 98 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1241 time to fit residues: 2.8156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 10309 Z= 0.119 Angle : 0.416 8.177 13877 Z= 0.218 Chirality : 0.038 0.139 1545 Planarity : 0.003 0.041 1765 Dihedral : 4.191 40.235 1356 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1233 helix: 1.43 (0.24), residues: 507 sheet: 0.84 (0.36), residues: 225 loop : -0.51 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 100 average time/residue: 0.2157 time to fit residues: 32.1673 Evaluate side-chains 94 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0977 time to fit residues: 2.1511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10309 Z= 0.220 Angle : 0.458 8.831 13877 Z= 0.237 Chirality : 0.039 0.176 1545 Planarity : 0.003 0.041 1765 Dihedral : 4.496 47.998 1356 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.27 % 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: 0.72 (0.25), residues: 1233 helix: 1.45 (0.24), residues: 505 sheet: 0.70 (0.36), residues: 224 loop : -0.57 (0.28), residues: 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 0.2305 time to fit residues: 31.3771 Evaluate side-chains 92 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1000 time to fit residues: 1.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10309 Z= 0.135 Angle : 0.421 5.899 13877 Z= 0.222 Chirality : 0.038 0.137 1545 Planarity : 0.003 0.041 1765 Dihedral : 4.342 44.717 1356 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1233 helix: 1.42 (0.24), residues: 508 sheet: 0.80 (0.36), residues: 223 loop : -0.51 (0.28), residues: 502 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.2250 time to fit residues: 32.3368 Evaluate side-chains 95 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0976 time to fit residues: 1.8114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.081422 restraints weight = 17997.132| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.79 r_work: 0.2892 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10309 Z= 0.114 Angle : 0.417 8.309 13877 Z= 0.217 Chirality : 0.038 0.130 1545 Planarity : 0.003 0.042 1765 Dihedral : 4.160 38.758 1356 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.00 % 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: 0.85 (0.25), residues: 1233 helix: 1.48 (0.24), residues: 508 sheet: 0.84 (0.36), residues: 224 loop : -0.46 (0.28), residues: 501 =============================================================================== Job complete usr+sys time: 1965.40 seconds wall clock time: 36 minutes 53.93 seconds (2213.93 seconds total)