Starting phenix.real_space_refine on Mon Jun 16 20:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chq_45598/06_2025/9chq_45598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chq_45598/06_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_45598/06_2025/9chq_45598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chq_45598/06_2025/9chq_45598.map" model { file = "/net/cci-nas-00/data/ceres_data/9chq_45598/06_2025/9chq_45598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chq_45598/06_2025/9chq_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-5710/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: 10.79, per 1000 atoms: 0.56 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: 4.61 Conformation dependent library (CDL) restraints added in 1.3 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: 1.26 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: 5.99 Time building geometry restraints manager: 5.57 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.570 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: 0.370 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 40.710 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.420 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15194 ( 692) hydrogen bonds : angle 6.66259 ( 2028) covalent geometry : bond 0.01286 ( 9776) covalent geometry : angle 1.73027 (13288) *********************** 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 : 1.442 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: 2.2937 time to fit residues: 593.5648 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 : 1.418 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.173587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110159 restraints weight = 29140.727| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.51 r_work: 0.2922 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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= 0.157 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 Details of bonding type rmsd hydrogen bonds : bond 0.05374 ( 692) hydrogen bonds : angle 4.48799 ( 2028) covalent geometry : bond 0.00327 ( 9776) covalent geometry : angle 0.56919 (13288) *********************** 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 : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 ASN cc_start: 0.7620 (t0) cc_final: 0.7267 (m-40) REVERT: B 691 ASN cc_start: 0.7619 (t0) cc_final: 0.7263 (m-40) REVERT: C 691 ASN cc_start: 0.7623 (t0) cc_final: 0.7272 (m-40) REVERT: D 691 ASN cc_start: 0.7615 (t0) cc_final: 0.7262 (m-40) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 1.9920 time to fit residues: 409.0183 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 : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.171527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.104180 restraints weight = 29132.920| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.18 r_work: 0.2891 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9776 Z= 0.191 Angle : 0.545 4.777 13288 Z= 0.302 Chirality : 0.040 0.137 1496 Planarity : 0.005 0.062 1620 Dihedral : 4.189 14.374 1280 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: 1.76 (0.25), residues: 1140 helix: 1.41 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.55 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 568 HIS 0.002 0.001 HIS A 687 PHE 0.013 0.002 PHE B 656 TYR 0.017 0.002 TYR A 611 ARG 0.008 0.001 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 692) hydrogen bonds : angle 4.25479 ( 2028) covalent geometry : bond 0.00434 ( 9776) covalent geometry : angle 0.54521 (13288) *********************** 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 : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6510 (tm) REVERT: A 688 GLN cc_start: 0.7919 (mp10) cc_final: 0.7704 (mp10) REVERT: A 691 ASN cc_start: 0.7372 (t0) cc_final: 0.7092 (m-40) REVERT: B 499 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6477 (tm) REVERT: B 688 GLN cc_start: 0.7858 (mp10) cc_final: 0.7653 (mp10) REVERT: B 691 ASN cc_start: 0.7418 (t0) cc_final: 0.7106 (m-40) REVERT: C 499 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6481 (tm) REVERT: C 688 GLN cc_start: 0.7925 (mp10) cc_final: 0.7711 (mp10) REVERT: C 691 ASN cc_start: 0.7421 (t0) cc_final: 0.7110 (m-40) REVERT: D 499 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6478 (tm) REVERT: D 688 GLN cc_start: 0.7917 (mp10) cc_final: 0.7701 (mp10) REVERT: D 691 ASN cc_start: 0.7429 (t0) cc_final: 0.7115 (m-40) outliers start: 18 outliers final: 4 residues processed: 180 average time/residue: 2.3440 time to fit residues: 460.0775 Evaluate side-chains 182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 18 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.174256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109728 restraints weight = 29250.239| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.67 r_work: 0.2917 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4059 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= 0.111 Angle : 0.452 4.489 13288 Z= 0.247 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.050 1620 Dihedral : 3.869 14.837 1280 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.47 % Allowed : 11.67 % Favored : 86.86 % 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: 2.25 (0.25), residues: 1140 helix: 1.76 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 0.65 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 568 HIS 0.004 0.001 HIS A 587 PHE 0.010 0.001 PHE A 656 TYR 0.014 0.001 TYR A 611 ARG 0.009 0.001 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 692) hydrogen bonds : angle 3.92413 ( 2028) covalent geometry : bond 0.00229 ( 9776) covalent geometry : angle 0.45177 (13288) *********************** 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 193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 688 GLN cc_start: 0.7781 (mp10) cc_final: 0.7527 (mp10) REVERT: B 499 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6428 (tm) REVERT: B 688 GLN cc_start: 0.7788 (mp10) cc_final: 0.7535 (mp10) REVERT: B 701 PHE cc_start: 0.8037 (t80) cc_final: 0.7827 (t80) REVERT: C 499 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6447 (tm) REVERT: C 688 GLN cc_start: 0.7789 (mp10) cc_final: 0.7537 (mp10) REVERT: D 499 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6440 (tm) REVERT: D 688 GLN cc_start: 0.7786 (mp10) cc_final: 0.7532 (mp10) REVERT: D 701 PHE cc_start: 0.8033 (t80) cc_final: 0.7826 (t80) outliers start: 15 outliers final: 4 residues processed: 178 average time/residue: 2.4539 time to fit residues: 478.0541 Evaluate side-chains 175 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.174681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108489 restraints weight = 28871.368| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.13 r_work: 0.2928 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9776 Z= 0.126 Angle : 0.464 4.441 13288 Z= 0.251 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.057 1620 Dihedral : 3.769 14.624 1280 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.18 % Allowed : 12.94 % Favored : 85.88 % 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: 2.39 (0.25), residues: 1140 helix: 1.86 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 0.72 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 568 HIS 0.002 0.001 HIS A 687 PHE 0.010 0.001 PHE B 656 TYR 0.015 0.001 TYR D 611 ARG 0.008 0.001 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 692) hydrogen bonds : angle 3.88369 ( 2028) covalent geometry : bond 0.00273 ( 9776) covalent geometry : angle 0.46397 (13288) *********************** 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 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6570 (mp) cc_final: 0.6310 (mp) REVERT: A 663 ILE cc_start: 0.7081 (mm) cc_final: 0.6784 (mt) REVERT: A 678 LEU cc_start: 0.7796 (mt) cc_final: 0.7410 (tt) REVERT: A 688 GLN cc_start: 0.7748 (mp10) cc_final: 0.7455 (mp10) REVERT: B 468 LEU cc_start: 0.6578 (mp) cc_final: 0.6353 (mp) REVERT: B 663 ILE cc_start: 0.7090 (mm) cc_final: 0.6792 (mt) REVERT: B 678 LEU cc_start: 0.7799 (mt) cc_final: 0.7413 (tt) REVERT: B 688 GLN cc_start: 0.7745 (mp10) cc_final: 0.7450 (mp10) REVERT: C 468 LEU cc_start: 0.6576 (mp) cc_final: 0.6350 (mp) REVERT: C 663 ILE cc_start: 0.7105 (mm) cc_final: 0.6805 (mt) REVERT: C 678 LEU cc_start: 0.7800 (mt) cc_final: 0.7416 (tt) REVERT: C 688 GLN cc_start: 0.7750 (mp10) cc_final: 0.7457 (mp10) REVERT: D 468 LEU cc_start: 0.6583 (mp) cc_final: 0.6355 (mp) REVERT: D 663 ILE cc_start: 0.7094 (mm) cc_final: 0.6794 (mt) REVERT: D 678 LEU cc_start: 0.7799 (mt) cc_final: 0.7412 (tt) REVERT: D 688 GLN cc_start: 0.7760 (mp10) cc_final: 0.7465 (mp10) outliers start: 12 outliers final: 4 residues processed: 175 average time/residue: 2.2764 time to fit residues: 431.8574 Evaluate side-chains 175 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain D residue 462 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.176416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109634 restraints weight = 28633.444| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.61 r_work: 0.2916 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9776 Z= 0.115 Angle : 0.452 4.343 13288 Z= 0.242 Chirality : 0.037 0.138 1496 Planarity : 0.004 0.062 1620 Dihedral : 3.670 14.972 1280 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.69 % Allowed : 14.22 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.26), residues: 1140 helix: 1.98 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 0.83 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 568 HIS 0.002 0.001 HIS A 687 PHE 0.010 0.001 PHE D 656 TYR 0.014 0.001 TYR A 611 ARG 0.009 0.001 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 692) hydrogen bonds : angle 3.79522 ( 2028) covalent geometry : bond 0.00246 ( 9776) covalent geometry : angle 0.45167 (13288) *********************** 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 180 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6509 (mp) cc_final: 0.6299 (mp) REVERT: A 499 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6431 (tm) REVERT: A 579 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5173 (mpt) REVERT: A 663 ILE cc_start: 0.7053 (mm) cc_final: 0.6760 (mt) REVERT: A 678 LEU cc_start: 0.7767 (mt) cc_final: 0.7391 (tt) REVERT: A 688 GLN cc_start: 0.7711 (mp10) cc_final: 0.7414 (mp10) REVERT: A 695 GLN cc_start: 0.6900 (mp10) cc_final: 0.6623 (mp10) REVERT: B 468 LEU cc_start: 0.6501 (mp) cc_final: 0.6293 (mp) REVERT: B 663 ILE cc_start: 0.7055 (mm) cc_final: 0.6763 (mt) REVERT: B 678 LEU cc_start: 0.7772 (mt) cc_final: 0.7396 (tt) REVERT: B 688 GLN cc_start: 0.7710 (mp10) cc_final: 0.7412 (mp10) REVERT: B 695 GLN cc_start: 0.6892 (mp10) cc_final: 0.6614 (mp10) REVERT: C 468 LEU cc_start: 0.6511 (mp) cc_final: 0.6300 (mp) REVERT: C 579 MET cc_start: 0.5462 (OUTLIER) cc_final: 0.5189 (mpt) REVERT: C 663 ILE cc_start: 0.7068 (mm) cc_final: 0.6772 (mt) REVERT: C 678 LEU cc_start: 0.7776 (mt) cc_final: 0.7401 (tt) REVERT: C 688 GLN cc_start: 0.7719 (mp10) cc_final: 0.7423 (mp10) REVERT: C 695 GLN cc_start: 0.6894 (mp10) cc_final: 0.6616 (mp10) REVERT: D 468 LEU cc_start: 0.6509 (mp) cc_final: 0.6298 (mp) REVERT: D 663 ILE cc_start: 0.7052 (mm) cc_final: 0.6754 (mt) REVERT: D 678 LEU cc_start: 0.7772 (mt) cc_final: 0.7398 (tt) REVERT: D 688 GLN cc_start: 0.7715 (mp10) cc_final: 0.7419 (mp10) REVERT: D 695 GLN cc_start: 0.6896 (mp10) cc_final: 0.6618 (mp10) outliers start: 7 outliers final: 4 residues processed: 173 average time/residue: 2.2069 time to fit residues: 413.4445 Evaluate side-chains 176 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 579 MET Chi-restraints excluded: chain D residue 462 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.177360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109610 restraints weight = 28512.980| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.62 r_work: 0.2913 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 9776 Z= 0.113 Angle : 0.448 4.301 13288 Z= 0.239 Chirality : 0.037 0.144 1496 Planarity : 0.005 0.067 1620 Dihedral : 3.610 15.143 1280 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.88 % Allowed : 14.31 % 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: 2.67 (0.26), residues: 1140 helix: 2.03 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.91 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 568 HIS 0.002 0.001 HIS C 687 PHE 0.009 0.001 PHE A 656 TYR 0.014 0.001 TYR A 611 ARG 0.009 0.001 ARG C 679 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 692) hydrogen bonds : angle 3.73318 ( 2028) covalent geometry : bond 0.00242 ( 9776) covalent geometry : angle 0.44781 (13288) *********************** 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 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6438 (mp) cc_final: 0.6231 (mp) REVERT: A 499 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6402 (tm) REVERT: A 579 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.5212 (mpt) REVERT: A 663 ILE cc_start: 0.7004 (mm) cc_final: 0.6717 (mt) REVERT: A 678 LEU cc_start: 0.7765 (mt) cc_final: 0.7401 (tt) REVERT: A 688 GLN cc_start: 0.7715 (mp10) cc_final: 0.7406 (mp10) REVERT: A 695 GLN cc_start: 0.6800 (mp10) cc_final: 0.6580 (mp10) REVERT: B 468 LEU cc_start: 0.6429 (mp) cc_final: 0.6222 (mp) REVERT: B 663 ILE cc_start: 0.7002 (mm) cc_final: 0.6719 (mt) REVERT: B 678 LEU cc_start: 0.7765 (mt) cc_final: 0.7401 (tt) REVERT: B 688 GLN cc_start: 0.7697 (mp10) cc_final: 0.7388 (mp10) REVERT: B 695 GLN cc_start: 0.6800 (mp10) cc_final: 0.6580 (mp10) REVERT: C 468 LEU cc_start: 0.6432 (mp) cc_final: 0.6223 (mp) REVERT: C 579 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.5227 (mpt) REVERT: C 663 ILE cc_start: 0.7009 (mm) cc_final: 0.6721 (mt) REVERT: C 678 LEU cc_start: 0.7772 (mt) cc_final: 0.7407 (tt) REVERT: C 688 GLN cc_start: 0.7719 (mp10) cc_final: 0.7411 (mp10) REVERT: C 695 GLN cc_start: 0.6808 (mp10) cc_final: 0.6588 (mp10) REVERT: D 468 LEU cc_start: 0.6437 (mp) cc_final: 0.6228 (mp) REVERT: D 663 ILE cc_start: 0.7003 (mm) cc_final: 0.6713 (mt) REVERT: D 678 LEU cc_start: 0.7768 (mt) cc_final: 0.7404 (tt) REVERT: D 688 GLN cc_start: 0.7700 (mp10) cc_final: 0.7394 (mp10) REVERT: D 695 GLN cc_start: 0.6809 (mp10) cc_final: 0.6588 (mp10) outliers start: 9 outliers final: 8 residues processed: 176 average time/residue: 2.2388 time to fit residues: 426.3367 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 : 1.394 ------------------------------------------------------------------------------- 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 C residue 579 MET Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 96 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.177943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109875 restraints weight = 28489.197| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.58 r_work: 0.2934 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4647 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= 0.106 Angle : 0.447 4.239 13288 Z= 0.237 Chirality : 0.036 0.128 1496 Planarity : 0.005 0.069 1620 Dihedral : 3.571 15.255 1280 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.69 % Allowed : 15.59 % Favored : 83.73 % 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: 2.78 (0.26), residues: 1140 helix: 2.10 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.96 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 568 HIS 0.002 0.001 HIS A 687 PHE 0.009 0.001 PHE C 656 TYR 0.013 0.001 TYR A 611 ARG 0.013 0.001 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 692) hydrogen bonds : angle 3.67572 ( 2028) covalent geometry : bond 0.00226 ( 9776) covalent geometry : angle 0.44730 (13288) *********************** 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: 7 poor density : 180 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LEU cc_start: 0.6498 (mp) cc_final: 0.6287 (mp) REVERT: A 499 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6336 (tm) REVERT: A 579 MET cc_start: 0.5504 (OUTLIER) cc_final: 0.5230 (mpt) REVERT: A 678 LEU cc_start: 0.7827 (mt) cc_final: 0.7457 (tt) REVERT: A 688 GLN cc_start: 0.7723 (mp10) cc_final: 0.7392 (mp10) REVERT: A 695 GLN cc_start: 0.6748 (mp10) cc_final: 0.6529 (mp10) REVERT: B 468 LEU cc_start: 0.6492 (mp) cc_final: 0.6283 (mp) REVERT: B 575 GLU cc_start: 0.7226 (mt-10) cc_final: 0.7016 (mt-10) REVERT: B 582 ARG cc_start: 0.6349 (mtp-110) cc_final: 0.5911 (mtm-85) REVERT: B 678 LEU cc_start: 0.7828 (mt) cc_final: 0.7456 (tt) REVERT: B 688 GLN cc_start: 0.7715 (mp10) cc_final: 0.7383 (mp10) REVERT: B 695 GLN cc_start: 0.6732 (mp10) cc_final: 0.6518 (mp10) REVERT: C 468 LEU cc_start: 0.6497 (mp) cc_final: 0.6286 (mp) REVERT: C 579 MET cc_start: 0.5472 (OUTLIER) cc_final: 0.5198 (mpt) REVERT: C 678 LEU cc_start: 0.7837 (mt) cc_final: 0.7468 (tt) REVERT: C 688 GLN cc_start: 0.7731 (mp10) cc_final: 0.7401 (mp10) REVERT: C 695 GLN cc_start: 0.6761 (mp10) cc_final: 0.6543 (mp10) REVERT: D 468 LEU cc_start: 0.6504 (mp) cc_final: 0.6294 (mp) REVERT: D 575 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6992 (mt-10) REVERT: D 582 ARG cc_start: 0.6347 (mtp-110) cc_final: 0.5910 (mtm-85) REVERT: D 678 LEU cc_start: 0.7834 (mt) cc_final: 0.7462 (tt) REVERT: D 688 GLN cc_start: 0.7725 (mp10) cc_final: 0.7391 (mp10) REVERT: D 695 GLN cc_start: 0.6753 (mp10) cc_final: 0.6534 (mp10) outliers start: 7 outliers final: 8 residues processed: 180 average time/residue: 2.7358 time to fit residues: 535.9263 Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 2.827 ------------------------------------------------------------------------------- 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 C residue 579 MET 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 13 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 97 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.177130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110481 restraints weight = 28305.309| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.65 r_work: 0.2928 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9776 Z= 0.115 Angle : 0.453 4.269 13288 Z= 0.240 Chirality : 0.037 0.129 1496 Planarity : 0.005 0.071 1620 Dihedral : 3.552 15.221 1280 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.69 % Allowed : 15.20 % Favored : 84.12 % 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: 2.82 (0.25), residues: 1140 helix: 2.14 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 0.95 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 568 HIS 0.002 0.001 HIS A 687 PHE 0.009 0.001 PHE B 656 TYR 0.013 0.001 TYR C 611 ARG 0.011 0.001 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 692) hydrogen bonds : angle 3.67926 ( 2028) covalent geometry : bond 0.00248 ( 9776) covalent geometry : angle 0.45286 (13288) *********************** 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 177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6330 (tm) REVERT: A 579 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.5215 (mpt) REVERT: A 688 GLN cc_start: 0.7688 (mp10) cc_final: 0.7368 (mp10) REVERT: B 582 ARG cc_start: 0.6356 (mtp-110) cc_final: 0.5907 (mtm-85) REVERT: B 688 GLN cc_start: 0.7684 (mp10) cc_final: 0.7362 (mp10) REVERT: C 468 LEU cc_start: 0.6503 (mp) cc_final: 0.6302 (mp) REVERT: C 579 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.5216 (mpt) REVERT: C 688 GLN cc_start: 0.7690 (mp10) cc_final: 0.7371 (mp10) REVERT: D 582 ARG cc_start: 0.6365 (mtp-110) cc_final: 0.5914 (mtm-85) REVERT: D 688 GLN cc_start: 0.7688 (mp10) cc_final: 0.7367 (mp10) outliers start: 7 outliers final: 8 residues processed: 170 average time/residue: 2.7762 time to fit residues: 511.5445 Evaluate side-chains 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 C residue 579 MET 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 3 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.174965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108278 restraints weight = 28407.284| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.46 r_work: 0.2903 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4670 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= 0.151 Angle : 0.484 4.338 13288 Z= 0.260 Chirality : 0.037 0.128 1496 Planarity : 0.005 0.069 1620 Dihedral : 3.638 14.786 1280 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.08 % Allowed : 14.80 % Favored : 84.12 % 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: 2.58 (0.26), residues: 1140 helix: 1.96 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 0.92 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 585 HIS 0.002 0.001 HIS D 687 PHE 0.011 0.001 PHE A 656 TYR 0.015 0.001 TYR A 611 ARG 0.011 0.001 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 692) hydrogen bonds : angle 3.77718 ( 2028) covalent geometry : bond 0.00340 ( 9776) covalent geometry : angle 0.48426 (13288) ********************** 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 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6359 (tm) REVERT: A 579 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.5023 (mpt) REVERT: A 688 GLN cc_start: 0.7727 (mp10) cc_final: 0.7418 (mp10) REVERT: B 582 ARG cc_start: 0.6354 (mtp-110) cc_final: 0.5908 (mtm-85) REVERT: B 688 GLN cc_start: 0.7725 (mp10) cc_final: 0.7414 (mp10) REVERT: C 579 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.5018 (mpt) REVERT: C 688 GLN cc_start: 0.7730 (mp10) cc_final: 0.7421 (mp10) REVERT: D 582 ARG cc_start: 0.6355 (mtp-110) cc_final: 0.5911 (mtm-85) REVERT: D 688 GLN cc_start: 0.7729 (mp10) cc_final: 0.7419 (mp10) outliers start: 11 outliers final: 8 residues processed: 178 average time/residue: 2.7776 time to fit residues: 537.8035 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 : 2.227 ------------------------------------------------------------------------------- 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 C residue 579 MET 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 108 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.175636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.108512 restraints weight = 28316.378| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.55 r_work: 0.2904 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4731 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= 0.139 Angle : 0.474 4.307 13288 Z= 0.254 Chirality : 0.037 0.129 1496 Planarity : 0.005 0.068 1620 Dihedral : 3.612 14.790 1280 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.08 % Allowed : 15.49 % Favored : 83.43 % 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: 2.60 (0.25), residues: 1140 helix: 1.99 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.84 (0.48), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 585 HIS 0.002 0.001 HIS A 687 PHE 0.011 0.001 PHE C 656 TYR 0.015 0.001 TYR D 611 ARG 0.011 0.001 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 692) hydrogen bonds : angle 3.77204 ( 2028) covalent geometry : bond 0.00310 ( 9776) covalent geometry : angle 0.47415 (13288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16278.05 seconds wall clock time: 285 minutes 22.83 seconds (17122.83 seconds total)