Starting phenix.real_space_refine on Tue Nov 19 09:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chq_45598/11_2024/9chq_45598.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chq_45598/11_2024/9chq_45598.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/9chq_45598/11_2024/9chq_45598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chq_45598/11_2024/9chq_45598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chq_45598/11_2024/9chq_45598.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chq_45598/11_2024/9chq_45598.cif" } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6292 2.51 5 N 1568 2.21 5 O 1600 1.98 5 H 9596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19104 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Restraints were copied for chains: C, B, D Time building chain proxies: 11.14, per 1000 atoms: 0.58 Number of scatterers: 19104 At special positions: 0 Unit cell: (122.85, 122.85, 93.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1600 8.00 N 1568 7.00 C 6292 6.00 H 9596 1.00 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 - 3.00 Amino acid : True - 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: 5.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 removed outlier: 3.512A pdb=" N LEU A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 450 through 472 removed outlier: 3.779A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 505 through 506 No H-bonds generated for 'chain 'A' and resid 505 through 506' Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.992A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 574 Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 606 through 624 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.659A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 688 Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.168A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 432 removed outlier: 3.512A pdb=" N LEU B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 472 removed outlier: 3.779A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 496 Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 505 through 506 No H-bonds generated for 'chain 'B' and resid 505 through 506' Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.991A pdb=" N VAL B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 574 Processing helix chain 'B' and resid 584 through 593 Processing helix chain 'B' and resid 606 through 624 Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.659A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 688 Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.168A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.513A pdb=" N LEU C 416 " --> pdb=" O TRP C 412 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 472 removed outlier: 3.779A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 496 Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 505 through 506 No H-bonds generated for 'chain 'C' and resid 505 through 506' Processing helix chain 'C' and resid 507 through 511 Processing helix chain 'C' and resid 517 through 525 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 538 removed outlier: 3.992A pdb=" N VAL C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 574 Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 606 through 624 Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.658A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 688 Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.168A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 3.512A pdb=" N LEU D 416 " --> pdb=" O TRP D 412 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 472 removed outlier: 3.779A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 496 Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 505 through 506 No H-bonds generated for 'chain 'D' and resid 505 through 506' Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 526 through 530 Processing helix chain 'D' and resid 531 through 538 removed outlier: 3.991A pdb=" N VAL D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 574 Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 606 through 624 Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.659A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 688 Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.168A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 2028 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: 6.79 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9580 1.13 - 1.30: 1524 1.30 - 1.48: 4047 1.48 - 1.65: 4141 1.65 - 1.82: 80 Bond restraints: 19372 Sorted by residual: bond pdb=" N LEU C 559 " pdb=" H LEU C 559 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CD2 HIS B 402 " pdb=" HD2 HIS B 402 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ILE B 521 " pdb=" H ILE B 521 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE D 521 " pdb=" H ILE D 521 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 TYR D 616 " pdb=" HE1 TYR D 616 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 29810 2.64 - 5.27: 3954 5.27 - 7.91: 1112 7.91 - 10.54: 20 10.54 - 13.18: 16 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CB HIS A 485 " pdb=" CG HIS A 485 " pdb=" CD2 HIS A 485 " ideal model delta sigma weight residual 131.20 125.15 6.05 1.30e+00 5.92e-01 2.16e+01 angle pdb=" CB HIS C 485 " pdb=" CG HIS C 485 " pdb=" CD2 HIS C 485 " ideal model delta sigma weight residual 131.20 125.15 6.05 1.30e+00 5.92e-01 2.16e+01 angle pdb=" CB HIS B 485 " pdb=" CG HIS B 485 " pdb=" CD2 HIS B 485 " ideal model delta sigma weight residual 131.20 125.15 6.05 1.30e+00 5.92e-01 2.16e+01 angle pdb=" CB HIS D 485 " pdb=" CG HIS D 485 " pdb=" CD2 HIS D 485 " ideal model delta sigma weight residual 131.20 125.15 6.05 1.30e+00 5.92e-01 2.16e+01 angle pdb=" CA ASN D 629 " pdb=" CB ASN D 629 " pdb=" CG ASN D 629 " ideal model delta sigma weight residual 112.60 117.19 -4.59 1.00e+00 1.00e+00 2.11e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.73: 8120 12.73 - 25.45: 688 25.45 - 38.18: 136 38.18 - 50.91: 104 50.91 - 63.64: 76 Dihedral angle restraints: 9124 sinusoidal: 4760 harmonic: 4364 Sorted by residual: dihedral pdb=" C SER A 624 " pdb=" N SER A 624 " pdb=" CA SER A 624 " pdb=" CB SER A 624 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" C SER B 624 " pdb=" N SER B 624 " pdb=" CA SER B 624 " pdb=" CB SER B 624 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" C SER C 624 " pdb=" N SER C 624 " pdb=" CA SER C 624 " pdb=" CB SER C 624 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 970 0.082 - 0.163: 446 0.163 - 0.245: 64 0.245 - 0.327: 12 0.327 - 0.408: 4 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA SER A 624 " pdb=" N SER A 624 " pdb=" C SER A 624 " pdb=" CB SER A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA SER C 624 " pdb=" N SER C 624 " pdb=" C SER C 624 " pdb=" CB SER C 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA SER B 624 " pdb=" N SER B 624 " pdb=" C SER B 624 " pdb=" CB SER B 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 1493 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 585 " -0.113 2.00e-02 2.50e+03 5.22e-02 1.09e+02 pdb=" CG TRP D 585 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 585 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP D 585 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP D 585 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TRP D 585 " 0.070 2.00e-02 2.50e+03 pdb=" CE3 TRP D 585 " 0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 585 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 585 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 585 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP D 585 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP D 585 " -0.079 2.00e-02 2.50e+03 pdb=" HE3 TRP D 585 " 0.018 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 585 " -0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 585 " -0.039 2.00e-02 2.50e+03 pdb=" HH2 TRP D 585 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 585 " -0.113 2.00e-02 2.50e+03 5.22e-02 1.09e+02 pdb=" CG TRP B 585 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 585 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 585 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP B 585 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TRP B 585 " 0.070 2.00e-02 2.50e+03 pdb=" CE3 TRP B 585 " 0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 585 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 585 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 585 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP B 585 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP B 585 " -0.079 2.00e-02 2.50e+03 pdb=" HE3 TRP B 585 " 0.018 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 585 " -0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 585 " -0.039 2.00e-02 2.50e+03 pdb=" HH2 TRP B 585 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 585 " -0.113 2.00e-02 2.50e+03 5.22e-02 1.09e+02 pdb=" CG TRP C 585 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 585 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP C 585 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP C 585 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TRP C 585 " 0.070 2.00e-02 2.50e+03 pdb=" CE3 TRP C 585 " 0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 585 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 585 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 585 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP C 585 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP C 585 " -0.079 2.00e-02 2.50e+03 pdb=" HE3 TRP C 585 " 0.018 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 585 " -0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 585 " -0.039 2.00e-02 2.50e+03 pdb=" HH2 TRP C 585 " -0.042 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 948 2.19 - 2.80: 33933 2.80 - 3.40: 53431 3.40 - 4.00: 70432 4.00 - 4.60: 100229 Nonbonded interactions: 258973 Sorted by model distance: nonbonded pdb=" OE2 GLU B 575 " pdb=" HG SER B 636 " model vdw 1.593 2.450 nonbonded pdb=" OE2 GLU A 575 " pdb=" HG SER A 636 " model vdw 1.593 2.450 nonbonded pdb=" OE2 GLU C 575 " pdb=" HG SER C 636 " model vdw 1.593 2.450 nonbonded pdb=" OE2 GLU D 575 " pdb=" HG SER D 636 " model vdw 1.593 2.450 nonbonded pdb=" HG SER D 620 " pdb=" O VAL D 625 " model vdw 1.616 2.450 ... (remaining 258968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.150 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: 0.350 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.970 Find NCS groups from input model: 0.720 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.013 0.044 9776 Z= 0.831 Angle : 1.730 7.344 13288 Z= 1.200 Chirality : 0.089 0.408 1496 Planarity : 0.016 0.155 1620 Dihedral : 11.630 63.038 3420 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.36 % 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: -0.39 (0.24), residues: 1140 helix: -0.20 (0.16), residues: 892 sheet: None (None), residues: 0 loop : 0.17 (0.46), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.016 TRP A 585 HIS 0.008 0.003 HIS D 587 PHE 0.063 0.012 PHE D 701 TYR 0.089 0.023 TYR D 611 ARG 0.007 0.001 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 GLN cc_start: 0.6981 (mt0) cc_final: 0.6700 (mm110) REVERT: A 691 ASN cc_start: 0.7994 (t0) cc_final: 0.7495 (m110) REVERT: A 700 TYR cc_start: 0.7633 (t80) cc_final: 0.7345 (t80) REVERT: B 664 GLN cc_start: 0.6980 (mt0) cc_final: 0.6701 (mm110) REVERT: B 691 ASN cc_start: 0.7992 (t0) cc_final: 0.7495 (m110) REVERT: B 700 TYR cc_start: 0.7633 (t80) cc_final: 0.7345 (t80) REVERT: C 664 GLN cc_start: 0.6979 (mt0) cc_final: 0.6699 (mm110) REVERT: C 691 ASN cc_start: 0.7990 (t0) cc_final: 0.7497 (m110) REVERT: C 700 TYR cc_start: 0.7638 (t80) cc_final: 0.7349 (t80) REVERT: D 664 GLN cc_start: 0.6984 (mt0) cc_final: 0.6701 (mm110) REVERT: D 691 ASN cc_start: 0.7991 (t0) cc_final: 0.7494 (m110) REVERT: D 700 TYR cc_start: 0.7638 (t80) cc_final: 0.7349 (t80) outliers start: 0 outliers final: 4 residues processed: 240 average time/residue: 2.4019 time to fit residues: 622.1454 Evaluate side-chains 165 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 464 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9776 Z= 0.208 Angle : 0.569 5.353 13288 Z= 0.321 Chirality : 0.040 0.147 1496 Planarity : 0.005 0.037 1620 Dihedral : 4.910 26.121 1288 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.39 % Allowed : 5.88 % Favored : 93.73 % 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: 1.54 (0.25), residues: 1140 helix: 1.20 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.68 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.003 0.001 HIS A 674 PHE 0.014 0.002 PHE D 656 TYR 0.017 0.002 TYR B 611 ARG 0.004 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 ASN cc_start: 0.7677 (t0) cc_final: 0.7304 (m-40) REVERT: B 691 ASN cc_start: 0.7674 (t0) cc_final: 0.7300 (m-40) REVERT: C 691 ASN cc_start: 0.7678 (t0) cc_final: 0.7302 (m-40) REVERT: D 691 ASN cc_start: 0.7677 (t0) cc_final: 0.7303 (m-40) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 2.0589 time to fit residues: 422.6262 Evaluate side-chains 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN A 695 GLN B 691 ASN B 695 GLN C 691 ASN C 695 GLN D 691 ASN D 695 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9776 Z= 0.286 Angle : 0.549 4.798 13288 Z= 0.305 Chirality : 0.040 0.138 1496 Planarity : 0.005 0.056 1620 Dihedral : 4.222 14.559 1280 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.76 % Allowed : 9.41 % Favored : 88.82 % 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: 1.72 (0.25), residues: 1140 helix: 1.40 (0.17), residues: 896 sheet: None (None), residues: 0 loop : 0.48 (0.46), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 585 HIS 0.002 0.001 HIS C 687 PHE 0.013 0.002 PHE B 656 TYR 0.016 0.002 TYR B 611 ARG 0.008 0.001 ARG A 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6526 (tm) REVERT: A 691 ASN cc_start: 0.7497 (t0) cc_final: 0.7173 (m-40) REVERT: B 499 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6499 (tm) REVERT: B 575 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 691 ASN cc_start: 0.7493 (t0) cc_final: 0.7182 (m-40) REVERT: C 499 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6499 (tm) REVERT: C 691 ASN cc_start: 0.7496 (t0) cc_final: 0.7183 (m-40) REVERT: D 499 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6497 (tm) REVERT: D 691 ASN cc_start: 0.7494 (t0) cc_final: 0.7181 (m-40) outliers start: 18 outliers final: 4 residues processed: 180 average time/residue: 2.2506 time to fit residues: 441.0555 Evaluate side-chains 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN B 695 GLN C 695 GLN D 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9776 Z= 0.230 Angle : 0.497 4.538 13288 Z= 0.275 Chirality : 0.039 0.135 1496 Planarity : 0.004 0.047 1620 Dihedral : 3.986 14.289 1280 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.76 % Allowed : 11.47 % Favored : 86.76 % 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: 1.97 (0.25), residues: 1140 helix: 1.57 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.58 (0.47), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 568 HIS 0.004 0.001 HIS A 587 PHE 0.012 0.001 PHE C 656 TYR 0.015 0.002 TYR C 611 ARG 0.008 0.001 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6448 (tm) REVERT: B 499 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6447 (tm) REVERT: C 499 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6447 (tm) REVERT: D 499 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6446 (tm) outliers start: 18 outliers final: 4 residues processed: 180 average time/residue: 2.3550 time to fit residues: 458.1435 Evaluate side-chains 170 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN B 695 GLN C 695 GLN D 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 9776 Z= 0.378 Angle : 0.574 4.732 13288 Z= 0.318 Chirality : 0.042 0.139 1496 Planarity : 0.005 0.055 1620 Dihedral : 4.092 15.164 1280 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.75 % Allowed : 11.08 % Favored : 86.18 % 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: 1.64 (0.26), residues: 1140 helix: 1.35 (0.17), residues: 896 sheet: None (None), residues: 0 loop : 0.40 (0.49), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 585 HIS 0.003 0.001 HIS A 562 PHE 0.012 0.002 PHE A 656 TYR 0.017 0.002 TYR A 611 ARG 0.009 0.001 ARG C 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6559 (tm) REVERT: B 499 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6530 (tm) REVERT: B 582 ARG cc_start: 0.6548 (mtp-110) cc_final: 0.6153 (mtm-85) REVERT: C 499 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6532 (tm) REVERT: D 499 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6530 (tm) REVERT: D 582 ARG cc_start: 0.6548 (mtp-110) cc_final: 0.6153 (mtm-85) outliers start: 28 outliers final: 4 residues processed: 172 average time/residue: 2.4658 time to fit residues: 457.7321 Evaluate side-chains 169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN B 695 GLN C 695 GLN D 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9776 Z= 0.204 Angle : 0.489 4.364 13288 Z= 0.266 Chirality : 0.038 0.134 1496 Planarity : 0.005 0.059 1620 Dihedral : 3.892 14.340 1280 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.08 % Allowed : 14.12 % Favored : 84.80 % 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: 1.97 (0.26), residues: 1140 helix: 1.60 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.41 (0.48), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 568 HIS 0.002 0.001 HIS A 587 PHE 0.011 0.001 PHE A 656 TYR 0.015 0.001 TYR A 611 ARG 0.007 0.001 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 LEU cc_start: 0.7896 (mt) cc_final: 0.7515 (tt) REVERT: A 691 ASN cc_start: 0.7325 (t0) cc_final: 0.7125 (m-40) REVERT: B 499 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6414 (tm) REVERT: B 582 ARG cc_start: 0.6690 (mtp-110) cc_final: 0.6313 (mtm-85) REVERT: B 678 LEU cc_start: 0.7896 (mt) cc_final: 0.7515 (tt) REVERT: B 691 ASN cc_start: 0.7324 (t0) cc_final: 0.7123 (m-40) REVERT: C 499 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6417 (tm) REVERT: C 678 LEU cc_start: 0.7896 (mt) cc_final: 0.7515 (tt) REVERT: D 499 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6413 (tm) REVERT: D 582 ARG cc_start: 0.6690 (mtp-110) cc_final: 0.6313 (mtm-85) REVERT: D 678 LEU cc_start: 0.7893 (mt) cc_final: 0.7516 (tt) outliers start: 11 outliers final: 4 residues processed: 174 average time/residue: 2.5186 time to fit residues: 473.1911 Evaluate side-chains 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.0010 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN B 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9776 Z= 0.145 Angle : 0.457 4.255 13288 Z= 0.244 Chirality : 0.037 0.136 1496 Planarity : 0.005 0.068 1620 Dihedral : 3.717 14.095 1280 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.08 % Allowed : 14.71 % Favored : 84.22 % 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: 2.44 (0.26), residues: 1140 helix: 1.91 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.66 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.002 0.001 HIS A 587 PHE 0.009 0.001 PHE B 656 TYR 0.014 0.001 TYR D 611 ARG 0.010 0.001 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6421 (tm) REVERT: A 579 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.5308 (mpt) REVERT: A 652 TYR cc_start: 0.7579 (m-80) cc_final: 0.7110 (m-80) REVERT: A 678 LEU cc_start: 0.7917 (mt) cc_final: 0.7546 (tt) REVERT: B 582 ARG cc_start: 0.6651 (mtp-110) cc_final: 0.6306 (mtm-85) REVERT: B 652 TYR cc_start: 0.7578 (m-80) cc_final: 0.7097 (m-80) REVERT: B 678 LEU cc_start: 0.7916 (mt) cc_final: 0.7547 (tt) REVERT: C 678 LEU cc_start: 0.7915 (mt) cc_final: 0.7548 (tt) REVERT: D 582 ARG cc_start: 0.6650 (mtp-110) cc_final: 0.6302 (mtm-85) REVERT: D 678 LEU cc_start: 0.7917 (mt) cc_final: 0.7546 (tt) outliers start: 11 outliers final: 6 residues processed: 183 average time/residue: 2.5793 time to fit residues: 507.9759 Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 695 GLN Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN B 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9776 Z= 0.215 Angle : 0.490 4.348 13288 Z= 0.264 Chirality : 0.038 0.127 1496 Planarity : 0.005 0.066 1620 Dihedral : 3.737 14.219 1280 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.98 % Allowed : 16.37 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.26), residues: 1140 helix: 1.80 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.64 (0.48), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.002 0.001 HIS C 687 PHE 0.011 0.001 PHE B 656 TYR 0.016 0.001 TYR D 611 ARG 0.009 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6506 (tm) REVERT: A 678 LEU cc_start: 0.7918 (mt) cc_final: 0.7557 (tt) REVERT: B 582 ARG cc_start: 0.6702 (mtp-110) cc_final: 0.6334 (mtm-85) REVERT: B 678 LEU cc_start: 0.7916 (mt) cc_final: 0.7554 (tt) REVERT: C 678 LEU cc_start: 0.7916 (mt) cc_final: 0.7556 (tt) REVERT: D 582 ARG cc_start: 0.6700 (mtp-110) cc_final: 0.6332 (mtm-85) REVERT: D 678 LEU cc_start: 0.7916 (mt) cc_final: 0.7556 (tt) outliers start: 10 outliers final: 9 residues processed: 174 average time/residue: 2.6080 time to fit residues: 488.4881 Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN B 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9776 Z= 0.166 Angle : 0.467 4.277 13288 Z= 0.249 Chirality : 0.037 0.125 1496 Planarity : 0.005 0.069 1620 Dihedral : 3.660 14.496 1280 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.98 % Allowed : 16.27 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.26), residues: 1140 helix: 1.91 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.63 (0.48), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS C 687 PHE 0.010 0.001 PHE C 656 TYR 0.014 0.001 TYR D 611 ARG 0.011 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6448 (tm) REVERT: A 501 ASP cc_start: 0.7847 (m-30) cc_final: 0.7544 (m-30) REVERT: A 651 MET cc_start: 0.7145 (mtp) cc_final: 0.6730 (ttm) REVERT: A 691 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.7004 (m-40) REVERT: B 582 ARG cc_start: 0.6668 (mtp-110) cc_final: 0.6316 (mtm-85) REVERT: B 651 MET cc_start: 0.7143 (mtp) cc_final: 0.6731 (ttm) REVERT: B 691 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.7010 (m-40) REVERT: C 651 MET cc_start: 0.7145 (mtp) cc_final: 0.6727 (ttm) REVERT: D 582 ARG cc_start: 0.6666 (mtp-110) cc_final: 0.6313 (mtm-85) REVERT: D 651 MET cc_start: 0.7147 (mtp) cc_final: 0.6729 (ttm) outliers start: 10 outliers final: 9 residues processed: 176 average time/residue: 1.9390 time to fit residues: 368.4766 Evaluate side-chains 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9776 Z= 0.247 Angle : 0.506 4.351 13288 Z= 0.275 Chirality : 0.038 0.126 1496 Planarity : 0.005 0.069 1620 Dihedral : 3.736 14.349 1280 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.98 % Allowed : 15.88 % Favored : 83.14 % 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: 2.16 (0.25), residues: 1140 helix: 1.72 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.51 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 585 HIS 0.002 0.001 HIS A 687 PHE 0.011 0.001 PHE C 656 TYR 0.014 0.002 TYR A 611 ARG 0.011 0.001 ARG A 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6480 (tm) REVERT: A 501 ASP cc_start: 0.7827 (m-30) cc_final: 0.7570 (m-30) REVERT: B 582 ARG cc_start: 0.6706 (mtp-110) cc_final: 0.6343 (mtm-85) REVERT: C 695 GLN cc_start: 0.6983 (mp10) cc_final: 0.6689 (mp10) REVERT: D 582 ARG cc_start: 0.6703 (mtp-110) cc_final: 0.6341 (mtm-85) REVERT: D 695 GLN cc_start: 0.6984 (mp10) cc_final: 0.6688 (mp10) outliers start: 10 outliers final: 9 residues processed: 183 average time/residue: 1.9464 time to fit residues: 384.8350 Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: