Starting phenix.real_space_refine on Wed Jun 18 12:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgv_36246/06_2025/8jgv_36246_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgv_36246/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jgv_36246/06_2025/8jgv_36246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgv_36246/06_2025/8jgv_36246.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgv_36246/06_2025/8jgv_36246_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgv_36246/06_2025/8jgv_36246_trim.cif" } resolution = 2.98 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= 0.033 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.42, per 1000 atoms: 0.49 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: 6.47 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.70 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: 7.55 Time building geometry restraints manager: 7.70 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: 0.07 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: 1.200 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: 0.410 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 47.340 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.850 ------------------------------------------------------------------------------- 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 : 9.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), 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 TRP 0.014 0.001 TRP B 403 HIS 0.003 0.001 HIS A 169 PHE 0.027 0.002 PHE A 377 TYR 0.023 0.001 TYR A 211 ARG 0.004 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.12563 ( 671) hydrogen bonds : angle 6.71653 ( 1989) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.67697 ( 8) covalent geometry : bond 0.00399 (10860) covalent geometry : angle 0.59881 (14752) *********************** 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 : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.6704 (m100) cc_final: 0.6413 (p-90) REVERT: A 615 MET cc_start: 0.7245 (mmt) cc_final: 0.6677 (mmt) REVERT: B 166 TRP cc_start: 0.6700 (m100) cc_final: 0.6414 (p-90) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 1.6999 time to fit residues: 324.7923 Evaluate side-chains 134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4425 r_free = 0.4425 target = 0.218699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175627 restraints weight = 31310.852| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.94 r_work: 0.3865 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10864 Z= 0.149 Angle : 0.537 7.271 14760 Z= 0.294 Chirality : 0.037 0.144 1666 Planarity : 0.005 0.053 1798 Dihedral : 7.872 53.138 1508 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.53 % Allowed : 8.72 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: 0.92 (0.24), residues: 1312 helix: 1.49 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -1.01 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 403 HIS 0.007 0.001 HIS A 552 PHE 0.036 0.001 PHE B 598 TYR 0.020 0.001 TYR B 550 ARG 0.003 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 671) hydrogen bonds : angle 5.18691 ( 1989) SS BOND : bond 0.00496 ( 4) SS BOND : angle 0.39990 ( 8) covalent geometry : bond 0.00331 (10860) covalent geometry : angle 0.53660 (14752) *********************** 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 157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.507 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: 0.8199 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: A 675 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.3948 (mpm) REVERT: B 158 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: B 675 MET cc_start: 0.4475 (OUTLIER) cc_final: 0.4004 (mpm) outliers start: 17 outliers final: 9 residues processed: 148 average time/residue: 1.5840 time to fit residues: 266.9649 Evaluate side-chains 148 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 425 LYS Chi-restraints excluded: chain A residue 515 VAL 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 425 LYS Chi-restraints excluded: chain B residue 515 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 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 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 = 0.4402 r_free = 0.4402 target = 0.216218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173015 restraints weight = 31356.779| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.94 r_work: 0.3865 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10864 Z= 0.196 Angle : 0.544 6.915 14760 Z= 0.297 Chirality : 0.038 0.161 1666 Planarity : 0.005 0.052 1798 Dihedral : 7.769 55.301 1508 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.98 % Allowed : 9.71 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.88 (0.24), residues: 1312 helix: 1.49 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.08 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 403 HIS 0.007 0.001 HIS A 552 PHE 0.032 0.002 PHE B 598 TYR 0.021 0.001 TYR A 211 ARG 0.002 0.000 ARG B 635 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 671) hydrogen bonds : angle 5.07508 ( 1989) SS BOND : bond 0.00521 ( 4) SS BOND : angle 0.64660 ( 8) covalent geometry : bond 0.00454 (10860) covalent geometry : angle 0.54377 (14752) *********************** 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 162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.595 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: 0.7236 (tpm170) cc_final: 0.6619 (mmp80) REVERT: A 158 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: A 670 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5228 (mt) REVERT: A 675 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.4029 (mpm) REVERT: B 95 ARG cc_start: 0.7328 (tpm170) cc_final: 0.6905 (mmm160) REVERT: B 158 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: B 670 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5268 (mt) REVERT: B 675 MET cc_start: 0.4599 (OUTLIER) cc_final: 0.4084 (mpm) outliers start: 22 outliers final: 5 residues processed: 153 average time/residue: 1.4888 time to fit residues: 260.9886 Evaluate side-chains 150 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 B residue 158 GLU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.217069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.173578 restraints weight = 31633.199| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.97 r_work: 0.3872 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10864 Z= 0.162 Angle : 0.517 6.757 14760 Z= 0.282 Chirality : 0.037 0.153 1666 Planarity : 0.005 0.052 1798 Dihedral : 7.531 54.176 1508 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.25 % Allowed : 11.69 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.99 (0.24), residues: 1312 helix: 1.61 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -1.13 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 403 HIS 0.007 0.001 HIS A 552 PHE 0.029 0.001 PHE A 598 TYR 0.019 0.001 TYR A 211 ARG 0.001 0.000 ARG B 635 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 671) hydrogen bonds : angle 4.86277 ( 1989) SS BOND : bond 0.00459 ( 4) SS BOND : angle 0.51904 ( 8) covalent geometry : bond 0.00371 (10860) covalent geometry : angle 0.51659 (14752) *********************** 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 165 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.468 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: 0.7938 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: A 395 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.4805 (mm) REVERT: A 555 TRP cc_start: 0.4884 (OUTLIER) cc_final: 0.4191 (m-10) REVERT: A 670 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.5271 (mt) REVERT: A 675 MET cc_start: 0.4530 (OUTLIER) cc_final: 0.4094 (mpm) REVERT: A 683 MET cc_start: 0.4487 (mmt) cc_final: 0.4267 (mmt) REVERT: A 773 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.6893 (m-30) REVERT: B 158 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 395 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.4767 (mm) REVERT: B 653 LEU cc_start: 0.7120 (mm) cc_final: 0.6784 (tp) REVERT: B 670 LEU cc_start: 0.5512 (OUTLIER) cc_final: 0.5264 (mt) REVERT: B 675 MET cc_start: 0.4532 (OUTLIER) cc_final: 0.4084 (mpm) REVERT: B 683 MET cc_start: 0.4445 (mmt) cc_final: 0.4230 (mmt) outliers start: 25 outliers final: 5 residues processed: 154 average time/residue: 1.5072 time to fit residues: 267.8530 Evaluate side-chains 152 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 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 129 optimal weight: 0.0980 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.217918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174612 restraints weight = 31423.509| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.98 r_work: 0.3867 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10864 Z= 0.122 Angle : 0.491 6.731 14760 Z= 0.267 Chirality : 0.036 0.147 1666 Planarity : 0.004 0.053 1798 Dihedral : 7.327 51.637 1508 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.07 % Allowed : 12.32 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.20 (0.24), residues: 1312 helix: 1.80 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.12 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 403 HIS 0.006 0.001 HIS A 552 PHE 0.025 0.001 PHE A 598 TYR 0.017 0.001 TYR A 211 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 671) hydrogen bonds : angle 4.68988 ( 1989) SS BOND : bond 0.00396 ( 4) SS BOND : angle 0.43103 ( 8) covalent geometry : bond 0.00271 (10860) covalent geometry : angle 0.49129 (14752) *********************** 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 162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.485 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: 0.5311 (OUTLIER) cc_final: 0.4791 (mm) REVERT: A 516 PHE cc_start: 0.8287 (m-80) cc_final: 0.8038 (m-80) REVERT: A 670 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5218 (mt) REVERT: A 675 MET cc_start: 0.4409 (OUTLIER) cc_final: 0.3969 (mpm) REVERT: B 516 PHE cc_start: 0.8265 (m-80) cc_final: 0.8033 (m-80) REVERT: B 555 TRP cc_start: 0.4964 (OUTLIER) cc_final: 0.4305 (m-10) REVERT: B 653 LEU cc_start: 0.7025 (mm) cc_final: 0.6671 (tp) REVERT: B 670 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5220 (mt) REVERT: B 675 MET cc_start: 0.4521 (OUTLIER) cc_final: 0.4092 (mpm) outliers start: 23 outliers final: 7 residues processed: 152 average time/residue: 1.4974 time to fit residues: 261.7619 Evaluate side-chains 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 652 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 675 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 80 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.217303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173310 restraints weight = 31432.217| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.99 r_work: 0.3882 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10864 Z= 0.148 Angle : 0.506 6.672 14760 Z= 0.274 Chirality : 0.037 0.150 1666 Planarity : 0.005 0.053 1798 Dihedral : 7.279 50.807 1508 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.07 % Allowed : 12.68 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.13 (0.24), residues: 1312 helix: 1.80 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 403 HIS 0.007 0.001 HIS A 552 PHE 0.028 0.001 PHE A 598 TYR 0.018 0.001 TYR A 211 ARG 0.002 0.000 ARG B 635 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 671) hydrogen bonds : angle 4.66455 ( 1989) SS BOND : bond 0.00403 ( 4) SS BOND : angle 0.58661 ( 8) covalent geometry : bond 0.00336 (10860) covalent geometry : angle 0.50635 (14752) *********************** 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 166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.592 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: A 516 PHE cc_start: 0.8271 (m-80) cc_final: 0.8016 (m-80) REVERT: A 670 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.5193 (mt) REVERT: A 675 MET cc_start: 0.4500 (OUTLIER) cc_final: 0.4060 (mpm) REVERT: A 773 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: B 516 PHE cc_start: 0.8254 (m-80) cc_final: 0.8015 (m-80) REVERT: B 555 TRP cc_start: 0.5006 (OUTLIER) cc_final: 0.4335 (m-10) REVERT: B 653 LEU cc_start: 0.7066 (mm) cc_final: 0.6687 (tp) REVERT: B 670 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.5207 (mt) REVERT: B 675 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.4104 (mpm) outliers start: 23 outliers final: 10 residues processed: 156 average time/residue: 1.8533 time to fit residues: 336.0258 Evaluate side-chains 152 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 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 652 THR 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 45 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.215473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.171288 restraints weight = 31583.646| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.98 r_work: 0.3857 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1629 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= 0.192 Angle : 0.536 6.601 14760 Z= 0.290 Chirality : 0.038 0.159 1666 Planarity : 0.005 0.056 1798 Dihedral : 7.413 51.865 1508 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.98 % Allowed : 13.40 % 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 (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: 0.96 (0.23), residues: 1312 helix: 1.63 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.25 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 403 HIS 0.007 0.001 HIS A 552 PHE 0.031 0.002 PHE A 598 TYR 0.023 0.002 TYR A 211 ARG 0.002 0.000 ARG B 635 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 671) hydrogen bonds : angle 4.74611 ( 1989) SS BOND : bond 0.00466 ( 4) SS BOND : angle 0.76779 ( 8) covalent geometry : bond 0.00447 (10860) covalent geometry : angle 0.53619 (14752) *********************** 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 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.644 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: A 166 TRP cc_start: 0.6721 (m100) cc_final: 0.6064 (p-90) REVERT: A 516 PHE cc_start: 0.8234 (m-80) cc_final: 0.8000 (m-80) REVERT: A 555 TRP cc_start: 0.4914 (OUTLIER) cc_final: 0.4363 (m-10) REVERT: A 670 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5292 (mt) REVERT: A 675 MET cc_start: 0.4493 (OUTLIER) cc_final: 0.4074 (mpm) REVERT: A 773 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: B 166 TRP cc_start: 0.6704 (m100) cc_final: 0.6062 (p-90) REVERT: B 516 PHE cc_start: 0.8227 (m-80) cc_final: 0.8005 (m-80) REVERT: B 555 TRP cc_start: 0.4990 (OUTLIER) cc_final: 0.4422 (m-10) REVERT: B 653 LEU cc_start: 0.7131 (mm) cc_final: 0.6774 (tp) REVERT: B 670 LEU cc_start: 0.5555 (OUTLIER) cc_final: 0.5243 (mt) REVERT: B 675 MET cc_start: 0.4475 (OUTLIER) cc_final: 0.4058 (mpm) outliers start: 22 outliers final: 10 residues processed: 151 average time/residue: 1.4838 time to fit residues: 256.8208 Evaluate side-chains 153 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 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 652 THR 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 63 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 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 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 = 0.4415 r_free = 0.4415 target = 0.217906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.174002 restraints weight = 31530.448| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.01 r_work: 0.3885 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10864 Z= 0.123 Angle : 0.494 6.631 14760 Z= 0.267 Chirality : 0.036 0.146 1666 Planarity : 0.004 0.055 1798 Dihedral : 7.199 49.407 1508 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 13.49 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 1.23 (0.24), residues: 1312 helix: 1.85 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 403 HIS 0.006 0.001 HIS A 552 PHE 0.024 0.001 PHE B 598 TYR 0.018 0.001 TYR A 211 ARG 0.001 0.000 ARG B 351 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 671) hydrogen bonds : angle 4.56385 ( 1989) SS BOND : bond 0.00381 ( 4) SS BOND : angle 0.44823 ( 8) covalent geometry : bond 0.00273 (10860) covalent geometry : angle 0.49419 (14752) *********************** 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 165 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.584 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: symmetry clash REVERT: A 395 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.4806 (mm) REVERT: A 516 PHE cc_start: 0.8311 (m-80) cc_final: 0.8088 (m-80) REVERT: A 555 TRP cc_start: 0.4849 (OUTLIER) cc_final: 0.4289 (m-10) REVERT: A 670 LEU cc_start: 0.5497 (OUTLIER) cc_final: 0.5173 (mt) REVERT: A 675 MET cc_start: 0.4487 (OUTLIER) cc_final: 0.4052 (mpm) REVERT: B 395 LEU cc_start: 0.5307 (OUTLIER) cc_final: 0.4758 (mm) REVERT: B 516 PHE cc_start: 0.8247 (m-80) cc_final: 0.8033 (m-80) REVERT: B 555 TRP cc_start: 0.4902 (OUTLIER) cc_final: 0.4332 (m-10) REVERT: B 653 LEU cc_start: 0.7164 (mm) cc_final: 0.6780 (tp) REVERT: B 670 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5161 (mt) REVERT: B 675 MET cc_start: 0.4554 (OUTLIER) cc_final: 0.4178 (mpm) outliers start: 23 outliers final: 8 residues processed: 156 average time/residue: 1.3909 time to fit residues: 250.2073 Evaluate side-chains 154 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.218064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.174066 restraints weight = 31504.480| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.99 r_work: 0.3870 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10864 Z= 0.135 Angle : 0.506 6.913 14760 Z= 0.272 Chirality : 0.036 0.149 1666 Planarity : 0.005 0.056 1798 Dihedral : 7.071 47.424 1508 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.89 % Allowed : 14.12 % 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 (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: 1.28 (0.24), residues: 1312 helix: 1.89 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 403 HIS 0.006 0.001 HIS A 552 PHE 0.026 0.001 PHE A 598 TYR 0.019 0.001 TYR A 211 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 671) hydrogen bonds : angle 4.54484 ( 1989) SS BOND : bond 0.00367 ( 4) SS BOND : angle 0.55787 ( 8) covalent geometry : bond 0.00306 (10860) covalent geometry : angle 0.50622 (14752) *********************** 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 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.651 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 95 ARG cc_start: 0.7013 (mmp80) cc_final: 0.6595 (mmm160) REVERT: A 166 TRP cc_start: 0.6747 (m100) cc_final: 0.6074 (p-90) REVERT: A 395 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.4815 (mm) REVERT: A 516 PHE cc_start: 0.8270 (m-80) cc_final: 0.8060 (m-80) REVERT: A 670 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5177 (mt) REVERT: A 675 MET cc_start: 0.4371 (OUTLIER) cc_final: 0.4058 (mpm) REVERT: B 95 ARG cc_start: 0.7076 (mmp80) cc_final: 0.6681 (mmm160) REVERT: B 166 TRP cc_start: 0.6721 (m100) cc_final: 0.6055 (p-90) REVERT: B 395 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4785 (mm) REVERT: B 516 PHE cc_start: 0.8223 (m-80) cc_final: 0.8021 (m-80) REVERT: B 555 TRP cc_start: 0.5023 (OUTLIER) cc_final: 0.4506 (m-10) REVERT: B 653 LEU cc_start: 0.7158 (mm) cc_final: 0.6786 (tp) REVERT: B 675 MET cc_start: 0.4370 (OUTLIER) cc_final: 0.4069 (mpm) outliers start: 21 outliers final: 7 residues processed: 156 average time/residue: 1.4660 time to fit residues: 263.9280 Evaluate side-chains 155 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 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 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 675 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4426 r_free = 0.4426 target = 0.219212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.175345 restraints weight = 31547.877| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.99 r_work: 0.3884 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1856 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= 0.120 Angle : 0.503 9.016 14760 Z= 0.269 Chirality : 0.036 0.145 1666 Planarity : 0.004 0.056 1798 Dihedral : 6.937 45.327 1508 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.35 % Allowed : 14.66 % 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 (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: 1.34 (0.24), residues: 1312 helix: 1.95 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 217 HIS 0.007 0.001 HIS A 552 PHE 0.024 0.001 PHE A 598 TYR 0.017 0.001 TYR A 211 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 671) hydrogen bonds : angle 4.51331 ( 1989) SS BOND : bond 0.00334 ( 4) SS BOND : angle 0.49588 ( 8) covalent geometry : bond 0.00266 (10860) covalent geometry : angle 0.50252 (14752) ********************** 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: 15 poor density : 144 time to evaluate : 1.793 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: A 166 TRP cc_start: 0.6735 (m100) cc_final: 0.6069 (p-90) REVERT: A 395 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.4740 (mm) REVERT: A 516 PHE cc_start: 0.8263 (m-80) cc_final: 0.8062 (m-80) REVERT: A 675 MET cc_start: 0.4402 (OUTLIER) cc_final: 0.4090 (mpm) REVERT: B 166 TRP cc_start: 0.6749 (m100) cc_final: 0.6065 (p-90) REVERT: B 174 TRP cc_start: 0.5534 (t60) cc_final: 0.4879 (p-90) REVERT: B 395 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.4709 (mm) REVERT: B 516 PHE cc_start: 0.8224 (m-80) cc_final: 0.7986 (m-80) REVERT: B 555 TRP cc_start: 0.5059 (OUTLIER) cc_final: 0.4545 (m-10) REVERT: B 653 LEU cc_start: 0.7057 (mm) cc_final: 0.6742 (tp) REVERT: B 670 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5228 (mt) REVERT: B 675 MET cc_start: 0.4417 (OUTLIER) cc_final: 0.4084 (mpm) outliers start: 15 outliers final: 6 residues processed: 153 average time/residue: 1.4477 time to fit residues: 256.0746 Evaluate side-chains 152 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET 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 675 MET Chi-restraints excluded: chain A residue 773 ASP 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 114 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.215720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171024 restraints weight = 31688.993| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.01 r_work: 0.3851 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10864 Z= 0.207 Angle : 0.565 8.076 14760 Z= 0.305 Chirality : 0.038 0.160 1666 Planarity : 0.005 0.056 1798 Dihedral : 7.087 46.638 1508 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.35 % Allowed : 14.93 % 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 (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: 0.97 (0.23), residues: 1312 helix: 1.62 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 403 HIS 0.007 0.001 HIS A 552 PHE 0.035 0.002 PHE A 598 TYR 0.025 0.002 TYR A 211 ARG 0.002 0.000 ARG B 710 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 671) hydrogen bonds : angle 4.76761 ( 1989) SS BOND : bond 0.00445 ( 4) SS BOND : angle 0.86273 ( 8) covalent geometry : bond 0.00487 (10860) covalent geometry : angle 0.56528 (14752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13490.79 seconds wall clock time: 231 minutes 12.83 seconds (13872.83 seconds total)