Starting phenix.real_space_refine on Sun Aug 24 16:13:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgv_36246/08_2025/8jgv_36246_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgv_36246/08_2025/8jgv_36246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jgv_36246/08_2025/8jgv_36246_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgv_36246/08_2025/8jgv_36246_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jgv_36246/08_2025/8jgv_36246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgv_36246/08_2025/8jgv_36246.map" } resolution = 2.98 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 70 5.16 5 C 6922 2.51 5 N 1738 2.21 5 O 1848 1.98 5 H 10630 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21214 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 10576 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 26, 'TRANS': 641} Chain breaks: 5 Chain: "B" Number of atoms: 10576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 10576 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 26, 'TRANS': 641} Chain breaks: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.40, per 1000 atoms: 0.21 Number of scatterers: 21214 At special positions: 0 Unit cell: (93.93, 90.21, 107.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 6 15.00 O 1848 8.00 N 1738 7.00 C 6922 6.00 H 10630 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 472 " distance=2.03 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: 2.11 Conformation dependent library (CDL) restraints added in 607.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 70.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.629A pdb=" N LYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 156 removed outlier: 4.627A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 203 through 233 Processing helix chain 'A' and resid 234 through 237 removed outlier: 3.574A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.659A pdb=" N THR A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.625A pdb=" N THR A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 346 through 366 removed outlier: 3.575A pdb=" N TRP A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 420 removed outlier: 3.515A pdb=" N PHE A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 443 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.582A pdb=" N ASP A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 518 removed outlier: 3.586A pdb=" N TYR A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.765A pdb=" N TRP A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.543A pdb=" N TYR A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.716A pdb=" N ILE A 634 " --> pdb=" O TYR A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.663A pdb=" N VAL A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 709 through 721 Processing helix chain 'A' and resid 767 through 779 removed outlier: 3.557A pdb=" N VAL A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'B' and resid 92 through 112 removed outlier: 3.614A pdb=" N LYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 156 removed outlier: 4.628A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 233 Processing helix chain 'B' and resid 234 through 237 removed outlier: 3.574A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.639A pdb=" N THR B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 283 through 298 removed outlier: 3.974A pdb=" N HIS B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.627A pdb=" N THR B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 327 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 346 through 366 removed outlier: 3.583A pdb=" N TRP B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 420 removed outlier: 3.518A pdb=" N PHE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.581A pdb=" N ASP B 473 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 518 removed outlier: 3.586A pdb=" N TYR B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.766A pdb=" N TRP B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.544A pdb=" N TYR B 574 " --> pdb=" O THR B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 628 through 636 removed outlier: 4.296A pdb=" N ILE B 634 " --> pdb=" O TYR B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 removed outlier: 3.634A pdb=" N VAL B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 687 Processing helix chain 'B' and resid 709 through 721 Processing helix chain 'B' and resid 767 through 779 Processing helix chain 'B' and resid 796 through 805 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 670 through 671 removed outlier: 6.082A pdb=" N LEU A 670 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 763 removed outlier: 6.163A pdb=" N VAL A 762 " --> pdb=" O THR A 786 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 671 removed outlier: 6.086A pdb=" N LEU B 670 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 761 through 763 removed outlier: 6.148A pdb=" N VAL B 762 " --> pdb=" O THR B 786 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1989 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: 5.10 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10606 1.03 - 1.23: 145 1.23 - 1.43: 4469 1.43 - 1.62: 6164 1.62 - 1.82: 106 Bond restraints: 21490 Sorted by residual: bond pdb=" N HIS A 633 " pdb=" CA HIS A 633 " ideal model delta sigma weight residual 1.456 1.477 -0.022 1.18e-02 7.18e+03 3.35e+00 bond pdb=" N HIS B 633 " pdb=" CA HIS B 633 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.16e-02 7.43e+03 2.92e+00 bond pdb=" CB PHE B 344 " pdb=" CG PHE B 344 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.92e+00 bond pdb=" CB PHE A 344 " pdb=" CG PHE A 344 " ideal model delta sigma weight residual 1.502 1.471 0.031 2.30e-02 1.89e+03 1.82e+00 bond pdb=" CD1 PHE A 344 " pdb=" CE1 PHE A 344 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.32e+00 ... (remaining 21485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.84: 38824 9.84 - 19.69: 2 19.69 - 29.53: 0 29.53 - 39.38: 0 39.38 - 49.22: 4 Bond angle restraints: 38830 Sorted by residual: angle pdb=" C HIS B 633 " pdb=" N ILE B 634 " pdb=" H ILE B 634 " ideal model delta sigma weight residual 123.57 74.35 49.22 3.00e+00 1.11e-01 2.69e+02 angle pdb=" C HIS A 633 " pdb=" N ILE A 634 " pdb=" CA ILE A 634 " ideal model delta sigma weight residual 123.08 139.64 -16.56 1.01e+00 9.80e-01 2.69e+02 angle pdb=" C HIS A 633 " pdb=" N ILE A 634 " pdb=" H ILE A 634 " ideal model delta sigma weight residual 123.61 74.43 49.18 3.00e+00 1.11e-01 2.69e+02 angle pdb=" CA ILE B 634 " pdb=" N ILE B 634 " pdb=" H ILE B 634 " ideal model delta sigma weight residual 113.27 64.97 48.30 3.00e+00 1.11e-01 2.59e+02 angle pdb=" CA ILE A 634 " pdb=" N ILE A 634 " pdb=" H ILE A 634 " ideal model delta sigma weight residual 113.31 65.22 48.09 3.00e+00 1.11e-01 2.57e+02 ... (remaining 38825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 9124 17.69 - 35.38: 666 35.38 - 53.07: 210 53.07 - 70.77: 104 70.77 - 88.46: 26 Dihedral angle restraints: 10130 sinusoidal: 5384 harmonic: 4746 Sorted by residual: dihedral pdb=" CA ARG A 659 " pdb=" C ARG A 659 " pdb=" N PRO A 660 " pdb=" CA PRO A 660 " ideal model delta harmonic sigma weight residual 180.00 147.03 32.97 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA ARG B 659 " pdb=" C ARG B 659 " pdb=" N PRO B 660 " pdb=" CA PRO B 660 " ideal model delta harmonic sigma weight residual 180.00 147.51 32.49 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA ILE B 253 " pdb=" C ILE B 253 " pdb=" N ARG B 254 " pdb=" CA ARG B 254 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 10127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1481 0.061 - 0.123: 164 0.123 - 0.184: 15 0.184 - 0.245: 0 0.245 - 0.306: 6 Chirality restraints: 1666 Sorted by residual: chirality pdb=" C2' ATP B 901 " pdb=" C1' ATP B 901 " pdb=" C3' ATP B 901 " pdb=" O2' ATP B 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ATP A 901 " pdb=" C1' ATP A 901 " pdb=" C3' ATP A 901 " pdb=" O2' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C3' ATP A 901 " pdb=" C2' ATP A 901 " pdb=" C4' ATP A 901 " pdb=" O3' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.89 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1663 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 283 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO A 284 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 283 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO B 284 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 608 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 609 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 609 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 609 " 0.028 5.00e-02 4.00e+02 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 260 2.07 - 2.70: 35129 2.70 - 3.34: 66584 3.34 - 3.97: 82011 3.97 - 4.60: 131878 Nonbonded interactions: 315862 Sorted by model distance: nonbonded pdb=" H ILE B 634 " pdb=" HA ILE B 634 " model vdw 1.438 1.816 nonbonded pdb=" H ILE A 634 " pdb=" HA ILE A 634 " model vdw 1.443 1.816 nonbonded pdb=" O ASN B 690 " pdb="HD21 ASN B 690 " model vdw 1.483 2.450 nonbonded pdb=" O ASN A 690 " pdb="HD21 ASN A 690 " model vdw 1.497 2.450 nonbonded pdb=" O VAL A 597 " pdb=" HG1 THR A 601 " model vdw 1.668 2.450 ... (remaining 315857 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 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 : 0.004 0.035 10864 Z= 0.177 Angle : 0.599 16.563 14760 Z= 0.359 Chirality : 0.041 0.306 1666 Planarity : 0.004 0.057 1798 Dihedral : 14.129 88.457 3872 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.71 (0.24), residues: 1312 helix: 1.16 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.023 0.001 TYR A 211 PHE 0.027 0.002 PHE A 377 TRP 0.014 0.001 TRP B 403 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00399 (10860) covalent geometry : angle 0.59881 (14752) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.67697 ( 8) hydrogen bonds : bond 0.12563 ( 671) hydrogen bonds : angle 6.71653 ( 1989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.585 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: A 615 MET cc_start: 0.7245 (mmt) cc_final: 0.6677 (mmt) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.9444 time to fit residues: 179.0506 Evaluate side-chains 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 171 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN B 168 ASN B 171 GLN ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.220484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176928 restraints weight = 31485.128| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.99 r_work: 0.3910 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10864 Z= 0.121 Angle : 0.517 7.539 14760 Z= 0.284 Chirality : 0.037 0.142 1666 Planarity : 0.005 0.051 1798 Dihedral : 7.707 51.450 1508 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.62 % Allowed : 8.54 % Favored : 89.84 % 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: 1.07 (0.24), residues: 1312 helix: 1.61 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.020 0.001 TYR B 550 PHE 0.032 0.001 PHE B 598 TRP 0.014 0.001 TRP B 403 HIS 0.005 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00258 (10860) covalent geometry : angle 0.51757 (14752) SS BOND : bond 0.00434 ( 4) SS BOND : angle 0.29389 ( 8) hydrogen bonds : bond 0.04254 ( 671) hydrogen bonds : angle 5.08031 ( 1989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.574 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: A 158 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: A 675 MET cc_start: 0.4401 (OUTLIER) cc_final: 0.3898 (mpm) REVERT: B 158 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: B 675 MET cc_start: 0.4462 (OUTLIER) cc_final: 0.3974 (mpm) outliers start: 18 outliers final: 6 residues processed: 154 average time/residue: 0.8040 time to fit residues: 141.0023 Evaluate side-chains 147 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.216514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.172140 restraints weight = 31410.347| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.98 r_work: 0.3867 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10864 Z= 0.190 Angle : 0.537 7.033 14760 Z= 0.294 Chirality : 0.038 0.156 1666 Planarity : 0.005 0.053 1798 Dihedral : 7.686 54.524 1508 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.62 % Allowed : 9.98 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.98 (0.24), residues: 1312 helix: 1.57 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -1.07 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 702 TYR 0.020 0.002 TYR A 211 PHE 0.033 0.002 PHE A 598 TRP 0.016 0.001 TRP B 403 HIS 0.005 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00438 (10860) covalent geometry : angle 0.53680 (14752) SS BOND : bond 0.00557 ( 4) SS BOND : angle 0.67527 ( 8) hydrogen bonds : bond 0.04355 ( 671) hydrogen bonds : angle 4.99299 ( 1989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.595 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: A 95 ARG cc_start: 0.7239 (tpm170) cc_final: 0.6804 (mmm160) REVERT: A 155 ASP cc_start: 0.7623 (m-30) cc_final: 0.7387 (m-30) REVERT: A 158 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 670 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.5157 (mt) REVERT: A 675 MET cc_start: 0.4543 (OUTLIER) cc_final: 0.4045 (mpm) REVERT: B 95 ARG cc_start: 0.7253 (tpm170) cc_final: 0.6816 (mmm160) REVERT: B 155 ASP cc_start: 0.7628 (m-30) cc_final: 0.7415 (m-30) REVERT: B 158 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: B 555 TRP cc_start: 0.4747 (OUTLIER) cc_final: 0.4088 (m-10) REVERT: B 670 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5185 (mt) REVERT: B 675 MET cc_start: 0.4564 (OUTLIER) cc_final: 0.4056 (mpm) outliers start: 18 outliers final: 7 residues processed: 149 average time/residue: 0.8021 time to fit residues: 135.9181 Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 773 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.219223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176414 restraints weight = 31311.582| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.94 r_work: 0.3897 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10864 Z= 0.125 Angle : 0.497 6.848 14760 Z= 0.271 Chirality : 0.036 0.148 1666 Planarity : 0.004 0.051 1798 Dihedral : 7.468 52.715 1508 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.80 % Allowed : 10.88 % Favored : 87.32 % 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: 1.16 (0.24), residues: 1312 helix: 1.74 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.06 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 702 TYR 0.017 0.001 TYR A 211 PHE 0.026 0.001 PHE B 598 TRP 0.013 0.001 TRP A 403 HIS 0.005 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00276 (10860) covalent geometry : angle 0.49739 (14752) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.41358 ( 8) hydrogen bonds : bond 0.03962 ( 671) hydrogen bonds : angle 4.79173 ( 1989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.410 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: A 395 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4778 (mm) REVERT: A 516 PHE cc_start: 0.8257 (m-80) cc_final: 0.8014 (m-80) REVERT: A 670 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5247 (mt) REVERT: A 675 MET cc_start: 0.4527 (OUTLIER) cc_final: 0.4024 (mpm) REVERT: A 683 MET cc_start: 0.4426 (mmt) cc_final: 0.4207 (mmt) REVERT: B 95 ARG cc_start: 0.7173 (tpm170) cc_final: 0.6571 (mmp80) REVERT: B 395 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.4748 (mm) REVERT: B 516 PHE cc_start: 0.8261 (m-80) cc_final: 0.8015 (m-80) REVERT: B 555 TRP cc_start: 0.4815 (OUTLIER) cc_final: 0.4124 (m-10) REVERT: B 653 LEU cc_start: 0.7038 (mm) cc_final: 0.6728 (tp) REVERT: B 670 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5247 (mt) REVERT: B 675 MET cc_start: 0.4570 (OUTLIER) cc_final: 0.4106 (mpm) REVERT: B 683 MET cc_start: 0.4502 (mmt) cc_final: 0.4290 (mmt) outliers start: 20 outliers final: 5 residues processed: 152 average time/residue: 0.6609 time to fit residues: 115.1777 Evaluate side-chains 146 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.214700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.170343 restraints weight = 31574.294| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.98 r_work: 0.3848 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10864 Z= 0.220 Angle : 0.561 6.716 14760 Z= 0.304 Chirality : 0.038 0.162 1666 Planarity : 0.005 0.052 1798 Dihedral : 7.664 54.899 1508 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.34 % Allowed : 12.59 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.85 (0.23), residues: 1312 helix: 1.54 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -1.26 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.023 0.002 TYR A 211 PHE 0.034 0.002 PHE B 598 TRP 0.017 0.001 TRP B 403 HIS 0.004 0.001 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00516 (10860) covalent geometry : angle 0.56086 (14752) SS BOND : bond 0.00518 ( 4) SS BOND : angle 0.81167 ( 8) hydrogen bonds : bond 0.04273 ( 671) hydrogen bonds : angle 4.90528 ( 1989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.619 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: A 158 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: A 555 TRP cc_start: 0.4907 (OUTLIER) cc_final: 0.4294 (m-10) REVERT: A 670 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5400 (mt) REVERT: A 675 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.4089 (mpm) REVERT: A 683 MET cc_start: 0.4368 (mmt) cc_final: 0.4167 (mmt) REVERT: A 773 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6873 (m-30) REVERT: B 158 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: B 166 TRP cc_start: 0.6712 (m100) cc_final: 0.6085 (p-90) REVERT: B 555 TRP cc_start: 0.4834 (OUTLIER) cc_final: 0.4258 (m-10) REVERT: B 653 LEU cc_start: 0.7105 (mm) cc_final: 0.6737 (tp) REVERT: B 670 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5382 (mt) REVERT: B 675 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4187 (mpm) REVERT: B 683 MET cc_start: 0.4456 (mmt) cc_final: 0.4245 (mmt) outliers start: 26 outliers final: 8 residues processed: 153 average time/residue: 0.7354 time to fit residues: 128.1094 Evaluate side-chains 150 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 TRP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 773 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.217738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174423 restraints weight = 31329.403| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.94 r_work: 0.3889 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10864 Z= 0.126 Angle : 0.494 6.661 14760 Z= 0.268 Chirality : 0.036 0.146 1666 Planarity : 0.005 0.055 1798 Dihedral : 7.387 52.487 1508 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.89 % Allowed : 12.59 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.12 (0.24), residues: 1312 helix: 1.78 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.25 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.019 0.001 TYR A 211 PHE 0.024 0.001 PHE B 598 TRP 0.014 0.001 TRP A 403 HIS 0.004 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00278 (10860) covalent geometry : angle 0.49393 (14752) SS BOND : bond 0.00390 ( 4) SS BOND : angle 0.46236 ( 8) hydrogen bonds : bond 0.03851 ( 671) hydrogen bonds : angle 4.65293 ( 1989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.336 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: A 395 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4835 (mm) REVERT: A 516 PHE cc_start: 0.8285 (m-80) cc_final: 0.8040 (m-80) REVERT: A 555 TRP cc_start: 0.4899 (OUTLIER) cc_final: 0.4228 (m-10) REVERT: A 670 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5160 (mt) REVERT: A 675 MET cc_start: 0.4475 (OUTLIER) cc_final: 0.4043 (mpm) REVERT: A 773 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.6827 (m-30) REVERT: B 166 TRP cc_start: 0.6717 (m100) cc_final: 0.6070 (p-90) REVERT: B 395 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.4774 (mm) REVERT: B 516 PHE cc_start: 0.8262 (m-80) cc_final: 0.8008 (m-80) REVERT: B 555 TRP cc_start: 0.4841 (OUTLIER) cc_final: 0.4250 (m-10) REVERT: B 653 LEU cc_start: 0.7055 (mm) cc_final: 0.6728 (tp) REVERT: B 670 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5156 (mt) REVERT: B 675 MET cc_start: 0.4542 (OUTLIER) cc_final: 0.4106 (mpm) outliers start: 21 outliers final: 6 residues processed: 150 average time/residue: 0.6479 time to fit residues: 110.8587 Evaluate side-chains 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 TRP Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 9.9990 chunk 118 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.218975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.175193 restraints weight = 31430.824| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.99 r_work: 0.3895 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10864 Z= 0.117 Angle : 0.484 6.665 14760 Z= 0.262 Chirality : 0.036 0.146 1666 Planarity : 0.004 0.056 1798 Dihedral : 7.159 49.048 1508 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.98 % Allowed : 12.95 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.31 (0.24), residues: 1312 helix: 1.92 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 351 TYR 0.017 0.001 TYR A 211 PHE 0.024 0.001 PHE A 598 TRP 0.013 0.001 TRP A 403 HIS 0.004 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00261 (10860) covalent geometry : angle 0.48373 (14752) SS BOND : bond 0.00328 ( 4) SS BOND : angle 0.46543 ( 8) hydrogen bonds : bond 0.03745 ( 671) hydrogen bonds : angle 4.53239 ( 1989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.361 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 158 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: A 395 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.4755 (mm) REVERT: A 516 PHE cc_start: 0.8315 (m-80) cc_final: 0.8108 (m-80) REVERT: A 555 TRP cc_start: 0.4906 (OUTLIER) cc_final: 0.4295 (m-10) REVERT: A 670 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5255 (mt) REVERT: A 675 MET cc_start: 0.4453 (OUTLIER) cc_final: 0.4039 (mpm) REVERT: B 395 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.4776 (mm) REVERT: B 555 TRP cc_start: 0.4859 (OUTLIER) cc_final: 0.4323 (m-10) REVERT: B 653 LEU cc_start: 0.7074 (mm) cc_final: 0.6741 (tp) REVERT: B 670 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5281 (mt) REVERT: B 675 MET cc_start: 0.4620 (OUTLIER) cc_final: 0.4271 (mpm) outliers start: 22 outliers final: 8 residues processed: 156 average time/residue: 0.5943 time to fit residues: 105.6461 Evaluate side-chains 152 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 TRP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 773 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.216677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.172635 restraints weight = 31290.500| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.98 r_work: 0.3871 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10864 Z= 0.174 Angle : 0.524 6.589 14760 Z= 0.282 Chirality : 0.037 0.155 1666 Planarity : 0.005 0.055 1798 Dihedral : 7.216 49.542 1508 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.07 % Allowed : 13.31 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.16 (0.24), residues: 1312 helix: 1.79 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.17 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 635 TYR 0.021 0.001 TYR A 211 PHE 0.031 0.001 PHE A 598 TRP 0.015 0.001 TRP B 403 HIS 0.003 0.001 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00407 (10860) covalent geometry : angle 0.52367 (14752) SS BOND : bond 0.00387 ( 4) SS BOND : angle 0.72365 ( 8) hydrogen bonds : bond 0.03982 ( 671) hydrogen bonds : angle 4.64427 ( 1989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.392 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: A 516 PHE cc_start: 0.8236 (m-80) cc_final: 0.7986 (m-80) REVERT: A 555 TRP cc_start: 0.4983 (OUTLIER) cc_final: 0.4418 (m-10) REVERT: A 670 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5255 (mt) REVERT: A 675 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.4019 (mpm) REVERT: B 95 ARG cc_start: 0.7227 (mmp80) cc_final: 0.6886 (mmm160) REVERT: B 166 TRP cc_start: 0.6688 (m100) cc_final: 0.6033 (p-90) REVERT: B 653 LEU cc_start: 0.6996 (mm) cc_final: 0.6702 (tp) REVERT: B 670 LEU cc_start: 0.5594 (OUTLIER) cc_final: 0.5285 (mt) REVERT: B 675 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.4049 (mpm) outliers start: 23 outliers final: 9 residues processed: 151 average time/residue: 0.6234 time to fit residues: 106.7365 Evaluate side-chains 147 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 TRP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.217501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.173385 restraints weight = 31308.180| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.99 r_work: 0.3875 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10864 Z= 0.155 Angle : 0.521 6.560 14760 Z= 0.280 Chirality : 0.037 0.150 1666 Planarity : 0.005 0.054 1798 Dihedral : 7.211 49.054 1508 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.62 % Allowed : 14.12 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.14 (0.24), residues: 1312 helix: 1.76 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.021 0.001 TYR A 211 PHE 0.028 0.001 PHE A 598 TRP 0.015 0.001 TRP B 403 HIS 0.003 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00355 (10860) covalent geometry : angle 0.52077 (14752) SS BOND : bond 0.00402 ( 4) SS BOND : angle 0.62329 ( 8) hydrogen bonds : bond 0.03921 ( 671) hydrogen bonds : angle 4.62803 ( 1989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.418 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 174 TRP cc_start: 0.5748 (t60) cc_final: 0.5084 (p-90) REVERT: A 516 PHE cc_start: 0.8258 (m-80) cc_final: 0.8011 (m-80) REVERT: A 555 TRP cc_start: 0.4973 (OUTLIER) cc_final: 0.4476 (m-10) REVERT: A 670 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.5273 (mt) REVERT: A 675 MET cc_start: 0.4362 (OUTLIER) cc_final: 0.4029 (mpm) REVERT: B 174 TRP cc_start: 0.5754 (t60) cc_final: 0.5091 (p-90) REVERT: B 653 LEU cc_start: 0.7016 (mm) cc_final: 0.6730 (tp) REVERT: B 670 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.5306 (mt) REVERT: B 675 MET cc_start: 0.4387 (OUTLIER) cc_final: 0.4061 (mpm) outliers start: 18 outliers final: 9 residues processed: 150 average time/residue: 0.5889 time to fit residues: 101.2512 Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 TRP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 91 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 690 ASN B 690 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.218555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174738 restraints weight = 31414.285| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.99 r_work: 0.3890 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10864 Z= 0.124 Angle : 0.509 8.449 14760 Z= 0.271 Chirality : 0.036 0.146 1666 Planarity : 0.005 0.055 1798 Dihedral : 7.032 46.396 1508 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.71 % Allowed : 14.30 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.28 (0.24), residues: 1312 helix: 1.89 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 351 TYR 0.018 0.001 TYR A 211 PHE 0.024 0.001 PHE A 598 TRP 0.012 0.001 TRP B 403 HIS 0.004 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00277 (10860) covalent geometry : angle 0.50917 (14752) SS BOND : bond 0.00343 ( 4) SS BOND : angle 0.48625 ( 8) hydrogen bonds : bond 0.03791 ( 671) hydrogen bonds : angle 4.55014 ( 1989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 607 is missing expected H atoms. Skipping. Residue THR 607 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.397 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: A 95 ARG cc_start: 0.7040 (mmp80) cc_final: 0.6681 (mmm160) REVERT: A 174 TRP cc_start: 0.5601 (t60) cc_final: 0.4910 (p-90) REVERT: A 395 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.4810 (mm) REVERT: A 555 TRP cc_start: 0.5029 (OUTLIER) cc_final: 0.4533 (m-10) REVERT: A 670 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5274 (mt) REVERT: A 675 MET cc_start: 0.4367 (OUTLIER) cc_final: 0.4051 (mpm) REVERT: B 95 ARG cc_start: 0.7018 (mmp80) cc_final: 0.6626 (mmm160) REVERT: B 174 TRP cc_start: 0.5585 (t60) cc_final: 0.4876 (p-90) REVERT: B 395 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.4769 (mm) REVERT: B 555 TRP cc_start: 0.4909 (OUTLIER) cc_final: 0.4439 (m-10) REVERT: B 653 LEU cc_start: 0.7027 (mm) cc_final: 0.6742 (tp) REVERT: B 670 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.5218 (mt) REVERT: B 675 MET cc_start: 0.4424 (OUTLIER) cc_final: 0.4095 (mpm) outliers start: 19 outliers final: 6 residues processed: 151 average time/residue: 0.6161 time to fit residues: 106.7680 Evaluate side-chains 150 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 555 TRP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 TRP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 0.0470 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.217651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.173358 restraints weight = 31274.319| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.00 r_work: 0.3876 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10864 Z= 0.157 Angle : 0.524 9.616 14760 Z= 0.281 Chirality : 0.037 0.152 1666 Planarity : 0.005 0.055 1798 Dihedral : 7.001 45.662 1508 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.71 % Allowed : 14.57 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.19 (0.24), residues: 1312 helix: 1.80 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 710 TYR 0.021 0.001 TYR A 211 PHE 0.029 0.001 PHE A 598 TRP 0.015 0.001 TRP A 217 HIS 0.004 0.001 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00360 (10860) covalent geometry : angle 0.52369 (14752) SS BOND : bond 0.00378 ( 4) SS BOND : angle 0.67839 ( 8) hydrogen bonds : bond 0.03912 ( 671) hydrogen bonds : angle 4.62168 ( 1989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6080.11 seconds wall clock time: 103 minutes 42.59 seconds (6222.59 seconds total)