Starting phenix.real_space_refine on Thu Sep 18 18:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chq_45598/09_2025/9chq_45598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chq_45598/09_2025/9chq_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/cci-nas-00/data/ceres_data/9chq_45598/09_2025/9chq_45598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chq_45598/09_2025/9chq_45598.map" model { file = "/net/cci-nas-00/data/ceres_data/9chq_45598/09_2025/9chq_45598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chq_45598/09_2025/9chq_45598.cif" } resolution = 3.0 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D Time building chain proxies: 4.71, per 1000 atoms: 0.25 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: 1.71 Conformation dependent library (CDL) restraints added in 507.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.53 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: 4.31 Time building geometry restraints manager: 2.40 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: 0.03 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: 1.740 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: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.250 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.150 ------------------------------------------------------------------------------- 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= 0.762 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG B 541 TYR 0.089 0.023 TYR D 611 PHE 0.063 0.012 PHE D 701 TRP 0.083 0.016 TRP A 585 HIS 0.008 0.003 HIS D 587 Details of bonding type rmsd covalent geometry : bond 0.01286 ( 9776) covalent geometry : angle 1.73027 (13288) hydrogen bonds : bond 0.15194 ( 692) hydrogen bonds : angle 6.66259 ( 2028) *********************** 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 : 0.626 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: 0.7496 (m110) REVERT: B 700 TYR cc_start: 0.7633 (t80) cc_final: 0.7346 (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: 1.2728 time to fit residues: 327.3543 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 : 0.500 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.173862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110373 restraints weight = 29370.562| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.39 r_work: 0.2928 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3013 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= 0.153 Angle : 0.572 5.409 13288 Z= 0.322 Chirality : 0.040 0.148 1496 Planarity : 0.005 0.036 1620 Dihedral : 4.930 26.401 1288 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.39 % Allowed : 6.27 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.25), residues: 1140 helix: 1.20 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.70 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 528 TYR 0.017 0.002 TYR C 611 PHE 0.015 0.002 PHE B 656 TRP 0.012 0.001 TRP A 568 HIS 0.003 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9776) covalent geometry : angle 0.57195 (13288) hydrogen bonds : bond 0.05439 ( 692) hydrogen bonds : angle 4.47104 ( 2028) *********************** 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 : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 ASN cc_start: 0.7624 (t0) cc_final: 0.7163 (m-40) REVERT: A 695 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: B 691 ASN cc_start: 0.7623 (t0) cc_final: 0.7261 (m-40) REVERT: C 691 ASN cc_start: 0.7625 (t0) cc_final: 0.7164 (m-40) REVERT: C 695 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: D 691 ASN cc_start: 0.7620 (t0) cc_final: 0.7160 (m-40) REVERT: D 695 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6848 (mp10) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 1.0929 time to fit residues: 222.9087 Evaluate side-chains 167 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain C residue 695 GLN Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.173385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108907 restraints weight = 29421.419| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.63 r_work: 0.2952 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 9776 Z= 0.131 Angle : 0.488 4.775 13288 Z= 0.269 Chirality : 0.038 0.136 1496 Planarity : 0.004 0.053 1620 Dihedral : 4.088 15.146 1280 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.96 % Allowed : 8.24 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.25), residues: 1140 helix: 1.59 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.69 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 679 TYR 0.015 0.002 TYR C 611 PHE 0.012 0.001 PHE D 656 TRP 0.012 0.001 TRP A 568 HIS 0.002 0.001 HIS D 578 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9776) covalent geometry : angle 0.48809 (13288) hydrogen bonds : bond 0.04482 ( 692) hydrogen bonds : angle 4.12902 ( 2028) *********************** 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: 20 poor density : 176 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 688 GLN cc_start: 0.7861 (mp10) cc_final: 0.7654 (mp10) REVERT: A 691 ASN cc_start: 0.7383 (t0) cc_final: 0.7076 (m-40) REVERT: B 575 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7154 (mt-10) REVERT: B 688 GLN cc_start: 0.7865 (mp10) cc_final: 0.7660 (mp10) REVERT: B 691 ASN cc_start: 0.7326 (t0) cc_final: 0.7096 (m-40) REVERT: C 575 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7156 (mt-10) REVERT: C 688 GLN cc_start: 0.7864 (mp10) cc_final: 0.7658 (mp10) REVERT: C 691 ASN cc_start: 0.7394 (t0) cc_final: 0.7086 (m-40) REVERT: D 575 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7145 (mt-10) REVERT: D 688 GLN cc_start: 0.7861 (mp10) cc_final: 0.7655 (mp10) REVERT: D 691 ASN cc_start: 0.7391 (t0) cc_final: 0.7084 (m-40) outliers start: 20 outliers final: 2 residues processed: 180 average time/residue: 1.1253 time to fit residues: 218.8905 Evaluate side-chains 173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain D residue 462 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 0.0470 chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.0030 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.5290 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.176081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110320 restraints weight = 28773.934| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.16 r_work: 0.2959 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 9776 Z= 0.099 Angle : 0.433 4.508 13288 Z= 0.235 Chirality : 0.036 0.137 1496 Planarity : 0.004 0.046 1620 Dihedral : 3.770 14.728 1280 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.96 % Allowed : 10.20 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.25), residues: 1140 helix: 1.87 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.96 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 679 TYR 0.013 0.001 TYR C 611 PHE 0.008 0.001 PHE D 656 TRP 0.010 0.001 TRP C 568 HIS 0.002 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 9776) covalent geometry : angle 0.43267 (13288) hydrogen bonds : bond 0.03866 ( 692) hydrogen bonds : angle 3.85376 ( 2028) *********************** 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 204 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6508 (mp) cc_final: 0.6275 (mp) REVERT: A 499 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6433 (tm) REVERT: A 688 GLN cc_start: 0.7716 (mp10) cc_final: 0.7483 (mp10) REVERT: A 701 PHE cc_start: 0.7827 (t80) cc_final: 0.7609 (t80) REVERT: B 468 LEU cc_start: 0.6455 (mp) cc_final: 0.6211 (mp) REVERT: B 499 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6415 (tm) REVERT: B 688 GLN cc_start: 0.7730 (mp10) cc_final: 0.7497 (mp10) REVERT: B 701 PHE cc_start: 0.7828 (t80) cc_final: 0.7611 (t80) REVERT: C 468 LEU cc_start: 0.6459 (mp) cc_final: 0.6213 (mp) REVERT: C 499 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6418 (tm) REVERT: C 688 GLN cc_start: 0.7723 (mp10) cc_final: 0.7490 (mp10) REVERT: D 400 ILE cc_start: 0.7043 (mm) cc_final: 0.6843 (mp) REVERT: D 468 LEU cc_start: 0.6469 (mp) cc_final: 0.6221 (mp) REVERT: D 499 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6418 (tm) REVERT: D 688 GLN cc_start: 0.7719 (mp10) cc_final: 0.7487 (mp10) outliers start: 20 outliers final: 3 residues processed: 188 average time/residue: 1.0019 time to fit residues: 204.5440 Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 176 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.174985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109702 restraints weight = 28841.066| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.38 r_work: 0.2918 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 9776 Z= 0.124 Angle : 0.453 4.471 13288 Z= 0.245 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.056 1620 Dihedral : 3.698 14.627 1280 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.65 % Allowed : 11.08 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.25), residues: 1140 helix: 1.89 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.96 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 679 TYR 0.014 0.001 TYR A 611 PHE 0.009 0.001 PHE B 656 TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9776) covalent geometry : angle 0.45348 (13288) hydrogen bonds : bond 0.03977 ( 692) hydrogen bonds : angle 3.85744 ( 2028) *********************** 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 203 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6656 (mp) cc_final: 0.6401 (mp) REVERT: A 499 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6422 (tm) REVERT: A 582 ARG cc_start: 0.5946 (mtp-110) cc_final: 0.5621 (mtm-85) REVERT: A 678 LEU cc_start: 0.7744 (mt) cc_final: 0.7370 (tt) REVERT: A 688 GLN cc_start: 0.7710 (mp10) cc_final: 0.7435 (mp10) REVERT: B 468 LEU cc_start: 0.6644 (mp) cc_final: 0.6393 (mp) REVERT: B 499 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6461 (tm) REVERT: B 678 LEU cc_start: 0.7746 (mt) cc_final: 0.7371 (tt) REVERT: B 688 GLN cc_start: 0.7701 (mp10) cc_final: 0.7420 (mp10) REVERT: C 468 LEU cc_start: 0.6645 (mp) cc_final: 0.6394 (mp) REVERT: C 499 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6457 (tm) REVERT: C 582 ARG cc_start: 0.5936 (mtp-110) cc_final: 0.5612 (mtm-85) REVERT: C 678 LEU cc_start: 0.7749 (mt) cc_final: 0.7373 (tt) REVERT: C 688 GLN cc_start: 0.7713 (mp10) cc_final: 0.7428 (mp10) REVERT: D 468 LEU cc_start: 0.6448 (mp) cc_final: 0.6205 (mp) REVERT: D 499 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6467 (tm) REVERT: D 678 LEU cc_start: 0.7750 (mt) cc_final: 0.7373 (tt) REVERT: D 688 GLN cc_start: 0.7708 (mp10) cc_final: 0.7435 (mp10) outliers start: 27 outliers final: 3 residues processed: 184 average time/residue: 1.0681 time to fit residues: 212.3165 Evaluate side-chains 182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 175 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 95 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.173888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111482 restraints weight = 28525.209| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.53 r_work: 0.2929 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4195 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= 0.144 Angle : 0.470 4.413 13288 Z= 0.254 Chirality : 0.037 0.137 1496 Planarity : 0.005 0.061 1620 Dihedral : 3.707 14.825 1280 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.88 % Allowed : 12.06 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.25), residues: 1140 helix: 1.87 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.00 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 679 TYR 0.015 0.001 TYR A 611 PHE 0.010 0.001 PHE C 656 TRP 0.011 0.001 TRP D 568 HIS 0.003 0.001 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9776) covalent geometry : angle 0.46984 (13288) hydrogen bonds : bond 0.04076 ( 692) hydrogen bonds : angle 3.86902 ( 2028) *********************** 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 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6589 (mp) cc_final: 0.6355 (mp) REVERT: A 499 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6492 (tm) REVERT: A 582 ARG cc_start: 0.6000 (mtp-110) cc_final: 0.5716 (mtm-85) REVERT: A 678 LEU cc_start: 0.7790 (mt) cc_final: 0.7410 (tt) REVERT: A 688 GLN cc_start: 0.7733 (mp10) cc_final: 0.7441 (mp10) REVERT: A 695 GLN cc_start: 0.6929 (mp10) cc_final: 0.6644 (mp10) REVERT: B 468 LEU cc_start: 0.6583 (mp) cc_final: 0.6351 (mp) REVERT: B 499 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6487 (tm) REVERT: B 582 ARG cc_start: 0.6095 (mtp-110) cc_final: 0.5802 (mtm-85) REVERT: B 678 LEU cc_start: 0.7788 (mt) cc_final: 0.7410 (tt) REVERT: B 688 GLN cc_start: 0.7730 (mp10) cc_final: 0.7431 (mp10) REVERT: C 468 LEU cc_start: 0.6573 (mp) cc_final: 0.6342 (mp) REVERT: C 499 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6485 (tm) REVERT: C 582 ARG cc_start: 0.6018 (mtp-110) cc_final: 0.5730 (mtm-85) REVERT: C 678 LEU cc_start: 0.7796 (mt) cc_final: 0.7420 (tt) REVERT: C 688 GLN cc_start: 0.7730 (mp10) cc_final: 0.7436 (mp10) REVERT: C 695 GLN cc_start: 0.6931 (mp10) cc_final: 0.6644 (mp10) REVERT: D 468 LEU cc_start: 0.6508 (mp) cc_final: 0.6295 (mp) REVERT: D 499 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6487 (tm) REVERT: D 582 ARG cc_start: 0.6099 (mtp-110) cc_final: 0.5807 (mtm-85) REVERT: D 678 LEU cc_start: 0.7790 (mt) cc_final: 0.7415 (tt) REVERT: D 688 GLN cc_start: 0.7729 (mp10) cc_final: 0.7441 (mp10) REVERT: D 695 GLN cc_start: 0.6938 (mp10) cc_final: 0.6655 (mp10) outliers start: 9 outliers final: 3 residues processed: 174 average time/residue: 1.0875 time to fit residues: 203.5798 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 : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 695 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.174770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109946 restraints weight = 28456.395| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.29 r_work: 0.2954 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.130 Angle : 0.461 4.312 13288 Z= 0.247 Chirality : 0.037 0.141 1496 Planarity : 0.005 0.065 1620 Dihedral : 3.647 14.752 1280 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.78 % Allowed : 13.53 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.25), residues: 1140 helix: 1.95 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.04 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 679 TYR 0.015 0.001 TYR A 611 PHE 0.010 0.001 PHE C 656 TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9776) covalent geometry : angle 0.46074 (13288) hydrogen bonds : bond 0.03968 ( 692) hydrogen bonds : angle 3.81397 ( 2028) *********************** 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 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6624 (mp) cc_final: 0.6400 (mp) REVERT: A 499 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6455 (tm) REVERT: A 582 ARG cc_start: 0.6046 (mtp-110) cc_final: 0.5741 (mtm-85) REVERT: A 663 ILE cc_start: 0.7091 (mm) cc_final: 0.6792 (mt) REVERT: A 678 LEU cc_start: 0.7827 (mt) cc_final: 0.7453 (tt) REVERT: A 688 GLN cc_start: 0.7672 (mp10) cc_final: 0.7360 (mp10) REVERT: A 695 GLN cc_start: 0.6889 (mp10) cc_final: 0.6653 (mp10) REVERT: B 499 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6461 (tm) REVERT: B 582 ARG cc_start: 0.6144 (mtp-110) cc_final: 0.5873 (mtm-85) REVERT: B 663 ILE cc_start: 0.7100 (mm) cc_final: 0.6801 (mt) REVERT: B 678 LEU cc_start: 0.7825 (mt) cc_final: 0.7451 (tt) REVERT: B 688 GLN cc_start: 0.7739 (mp10) cc_final: 0.7432 (mp10) REVERT: C 499 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6459 (tm) REVERT: C 582 ARG cc_start: 0.6050 (mtp-110) cc_final: 0.5743 (mtm-85) REVERT: C 663 ILE cc_start: 0.7106 (mm) cc_final: 0.6805 (mt) REVERT: C 678 LEU cc_start: 0.7835 (mt) cc_final: 0.7460 (tt) REVERT: C 688 GLN cc_start: 0.7739 (mp10) cc_final: 0.7434 (mp10) REVERT: C 695 GLN cc_start: 0.6895 (mp10) cc_final: 0.6662 (mp10) REVERT: D 499 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6456 (tm) REVERT: D 582 ARG cc_start: 0.6147 (mtp-110) cc_final: 0.5875 (mtm-85) REVERT: D 663 ILE cc_start: 0.7109 (mm) cc_final: 0.6803 (mt) REVERT: D 678 LEU cc_start: 0.7834 (mt) cc_final: 0.7457 (tt) REVERT: D 688 GLN cc_start: 0.7727 (mp10) cc_final: 0.7424 (mp10) REVERT: D 695 GLN cc_start: 0.6898 (mp10) cc_final: 0.6663 (mp10) outliers start: 8 outliers final: 4 residues processed: 176 average time/residue: 1.0819 time to fit residues: 205.3824 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 : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 695 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 695 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110451 restraints weight = 28582.704| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.49 r_work: 0.2934 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9776 Z= 0.102 Angle : 0.439 4.239 13288 Z= 0.234 Chirality : 0.036 0.140 1496 Planarity : 0.005 0.068 1620 Dihedral : 3.557 14.937 1280 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.78 % Allowed : 13.82 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.25), residues: 1140 helix: 2.11 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.12 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 679 TYR 0.012 0.001 TYR B 611 PHE 0.009 0.001 PHE D 656 TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS B 687 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9776) covalent geometry : angle 0.43897 (13288) hydrogen bonds : bond 0.03757 ( 692) hydrogen bonds : angle 3.70370 ( 2028) *********************** 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 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6470 (mp) cc_final: 0.6265 (mp) REVERT: A 499 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6399 (tm) REVERT: A 582 ARG cc_start: 0.5949 (mtp-110) cc_final: 0.5679 (mtm-85) REVERT: A 663 ILE cc_start: 0.7027 (mm) cc_final: 0.6740 (mt) REVERT: A 678 LEU cc_start: 0.7787 (mt) cc_final: 0.7418 (tt) REVERT: A 688 GLN cc_start: 0.7701 (mp10) cc_final: 0.7378 (mp10) REVERT: A 695 GLN cc_start: 0.6730 (mp10) cc_final: 0.6505 (mp10) REVERT: B 499 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6400 (tm) REVERT: B 663 ILE cc_start: 0.7034 (mm) cc_final: 0.6744 (mt) REVERT: B 678 LEU cc_start: 0.7787 (mt) cc_final: 0.7418 (tt) REVERT: B 688 GLN cc_start: 0.7691 (mp10) cc_final: 0.7373 (mp10) REVERT: C 499 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6400 (tm) REVERT: C 582 ARG cc_start: 0.5958 (mtp-110) cc_final: 0.5684 (mtm-85) REVERT: C 663 ILE cc_start: 0.7040 (mm) cc_final: 0.6749 (mt) REVERT: C 678 LEU cc_start: 0.7791 (mt) cc_final: 0.7425 (tt) REVERT: C 688 GLN cc_start: 0.7657 (mp10) cc_final: 0.7327 (mp10) REVERT: C 695 GLN cc_start: 0.6729 (mp10) cc_final: 0.6505 (mp10) REVERT: D 499 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6397 (tm) REVERT: D 663 ILE cc_start: 0.7041 (mm) cc_final: 0.6745 (mt) REVERT: D 678 LEU cc_start: 0.7792 (mt) cc_final: 0.7424 (tt) REVERT: D 688 GLN cc_start: 0.7702 (mp10) cc_final: 0.7379 (mp10) REVERT: D 695 GLN cc_start: 0.6733 (mp10) cc_final: 0.6509 (mp10) outliers start: 8 outliers final: 7 residues processed: 179 average time/residue: 1.1910 time to fit residues: 229.0810 Evaluate side-chains 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN A 587 HIS B 695 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.173847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106324 restraints weight = 28338.619| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.43 r_work: 0.2897 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9776 Z= 0.164 Angle : 0.487 4.392 13288 Z= 0.263 Chirality : 0.038 0.129 1496 Planarity : 0.005 0.068 1620 Dihedral : 3.653 14.439 1280 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.88 % Allowed : 14.61 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.25), residues: 1140 helix: 1.91 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.03 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 582 TYR 0.015 0.002 TYR A 611 PHE 0.011 0.001 PHE D 656 TRP 0.012 0.001 TRP C 585 HIS 0.002 0.001 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9776) covalent geometry : angle 0.48736 (13288) hydrogen bonds : bond 0.04112 ( 692) hydrogen bonds : angle 3.82926 ( 2028) *********************** 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 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6673 (mp) cc_final: 0.6456 (mp) REVERT: A 499 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6465 (tm) REVERT: A 663 ILE cc_start: 0.7059 (mm) cc_final: 0.6771 (mt) REVERT: A 678 LEU cc_start: 0.7803 (mt) cc_final: 0.7430 (tt) REVERT: A 688 GLN cc_start: 0.7724 (mp10) cc_final: 0.7418 (mp10) REVERT: A 695 GLN cc_start: 0.6720 (mp10) cc_final: 0.6512 (mp10) REVERT: B 499 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6469 (tm) REVERT: B 582 ARG cc_start: 0.6072 (mtp-110) cc_final: 0.5824 (mtm-85) REVERT: B 663 ILE cc_start: 0.7064 (mm) cc_final: 0.6775 (mt) REVERT: B 678 LEU cc_start: 0.7797 (mt) cc_final: 0.7423 (tt) REVERT: B 688 GLN cc_start: 0.7729 (mp10) cc_final: 0.7421 (mp10) REVERT: C 499 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6462 (tm) REVERT: C 663 ILE cc_start: 0.7071 (mm) cc_final: 0.6781 (mt) REVERT: C 678 LEU cc_start: 0.7826 (mt) cc_final: 0.7455 (tt) REVERT: C 688 GLN cc_start: 0.7686 (mp10) cc_final: 0.7379 (mp10) REVERT: C 695 GLN cc_start: 0.6725 (mp10) cc_final: 0.6519 (mp10) REVERT: D 499 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6458 (tm) REVERT: D 582 ARG cc_start: 0.6069 (mtp-110) cc_final: 0.5822 (mtm-85) REVERT: D 663 ILE cc_start: 0.7078 (mm) cc_final: 0.6781 (mt) REVERT: D 678 LEU cc_start: 0.7825 (mt) cc_final: 0.7451 (tt) REVERT: D 688 GLN cc_start: 0.7729 (mp10) cc_final: 0.7422 (mp10) REVERT: D 695 GLN cc_start: 0.6731 (mp10) cc_final: 0.6523 (mp10) outliers start: 9 outliers final: 7 residues processed: 180 average time/residue: 1.1453 time to fit residues: 222.3895 Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 695 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.175487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.107189 restraints weight = 28511.063| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.18 r_work: 0.2925 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4496 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= 0.119 Angle : 0.457 4.264 13288 Z= 0.243 Chirality : 0.037 0.132 1496 Planarity : 0.005 0.070 1620 Dihedral : 3.583 14.470 1280 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.78 % Allowed : 14.71 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.26), residues: 1140 helix: 2.02 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.09 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 582 TYR 0.013 0.001 TYR A 611 PHE 0.009 0.001 PHE D 656 TRP 0.011 0.001 TRP A 568 HIS 0.002 0.001 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9776) covalent geometry : angle 0.45706 (13288) hydrogen bonds : bond 0.03856 ( 692) hydrogen bonds : angle 3.73972 ( 2028) ********************** 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 188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6375 (tm) REVERT: A 663 ILE cc_start: 0.7087 (mm) cc_final: 0.6797 (mt) REVERT: A 688 GLN cc_start: 0.7696 (mp10) cc_final: 0.7381 (mp10) REVERT: A 695 GLN cc_start: 0.6779 (mp10) cc_final: 0.6556 (mp10) REVERT: B 499 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6379 (tm) REVERT: B 663 ILE cc_start: 0.7088 (mm) cc_final: 0.6798 (mt) REVERT: B 688 GLN cc_start: 0.7727 (mp10) cc_final: 0.7424 (mp10) REVERT: C 499 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6377 (tm) REVERT: C 663 ILE cc_start: 0.7098 (mm) cc_final: 0.6805 (mt) REVERT: C 688 GLN cc_start: 0.7630 (mp10) cc_final: 0.7326 (mp10) REVERT: C 695 GLN cc_start: 0.6780 (mp10) cc_final: 0.6564 (mp10) REVERT: D 499 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6372 (tm) REVERT: D 663 ILE cc_start: 0.7099 (mm) cc_final: 0.6804 (mt) REVERT: D 688 GLN cc_start: 0.7707 (mp10) cc_final: 0.7393 (mp10) REVERT: D 695 GLN cc_start: 0.6789 (mp10) cc_final: 0.6570 (mp10) outliers start: 8 outliers final: 7 residues processed: 180 average time/residue: 1.2083 time to fit residues: 234.3819 Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 0.0060 chunk 111 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 68 optimal weight: 0.0030 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 695 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.175361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106952 restraints weight = 28510.051| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.15 r_work: 0.2923 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 9776 Z= 0.122 Angle : 0.453 4.288 13288 Z= 0.242 Chirality : 0.037 0.132 1496 Planarity : 0.005 0.070 1620 Dihedral : 3.527 14.577 1280 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.78 % Allowed : 15.20 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.25), residues: 1140 helix: 2.05 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.11 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 679 TYR 0.014 0.001 TYR B 611 PHE 0.010 0.001 PHE B 656 TRP 0.011 0.001 TRP B 568 HIS 0.002 0.001 HIS C 687 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9776) covalent geometry : angle 0.45326 (13288) hydrogen bonds : bond 0.03826 ( 692) hydrogen bonds : angle 3.72041 ( 2028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7596.67 seconds wall clock time: 128 minutes 56.44 seconds (7736.44 seconds total)