Starting phenix.real_space_refine on Wed May 21 08:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jgv_36246/05_2025/8jgv_36246_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jgv_36246/05_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_36246/05_2025/8jgv_36246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jgv_36246/05_2025/8jgv_36246.map" model { file = "/net/cci-nas-00/data/ceres_data/8jgv_36246/05_2025/8jgv_36246_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jgv_36246/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.13, per 1000 atoms: 0.48 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: 6.63 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: 1.88 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: 7.83 Time building geometry restraints manager: 7.78 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.340 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.350 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.710 ------------------------------------------------------------------------------- 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 : 1.604 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: 1.7080 time to fit residues: 326.2596 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 : 1.457 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175635 restraints weight = 31310.828| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.94 r_work: 0.3865 rms_B_bonded: 2.69 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: 0.7043 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 5.18690 ( 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 : 1.503 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: 0.7570 (mt-10) REVERT: A 675 MET cc_start: 0.4437 (OUTLIER) cc_final: 0.3941 (mpm) REVERT: B 158 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: B 675 MET cc_start: 0.4472 (OUTLIER) cc_final: 0.4000 (mpm) outliers start: 17 outliers final: 9 residues processed: 148 average time/residue: 1.5471 time to fit residues: 260.4488 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 : 1.486 ------------------------------------------------------------------------------- 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: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4403 r_free = 0.4403 target = 0.216439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172513 restraints weight = 31298.385| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.97 r_work: 0.3864 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1207 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= 0.195 Angle : 0.545 6.939 14760 Z= 0.297 Chirality : 0.038 0.158 1666 Planarity : 0.005 0.052 1798 Dihedral : 7.766 55.442 1508 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.98 % Allowed : 9.62 % 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 (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 0.017 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 0.04369 ( 671) hydrogen bonds : angle 5.06843 ( 1989) SS BOND : bond 0.00518 ( 4) SS BOND : angle 0.64264 ( 8) covalent geometry : bond 0.00453 (10860) covalent geometry : angle 0.54463 (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 : 1.589 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: 0.7251 (tpm170) cc_final: 0.6624 (mmp80) REVERT: A 158 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: A 670 LEU cc_start: 0.5429 (OUTLIER) cc_final: 0.5218 (mt) REVERT: A 675 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.4011 (mpm) REVERT: B 95 ARG cc_start: 0.7337 (tpm170) cc_final: 0.6919 (mmm160) REVERT: B 158 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: B 675 MET cc_start: 0.4552 (OUTLIER) cc_final: 0.4009 (mpm) outliers start: 22 outliers final: 5 residues processed: 153 average time/residue: 1.4965 time to fit residues: 261.5417 Evaluate side-chains 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 675 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.215771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171694 restraints weight = 31616.656| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.97 r_work: 0.3864 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10864 Z= 0.176 Angle : 0.528 6.755 14760 Z= 0.288 Chirality : 0.037 0.154 1666 Planarity : 0.005 0.053 1798 Dihedral : 7.579 54.886 1508 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.25 % Allowed : 11.96 % Favored : 85.79 % 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: 0.92 (0.24), residues: 1312 helix: 1.56 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 403 HIS 0.009 0.001 HIS A 552 PHE 0.030 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 0.04108 ( 671) hydrogen bonds : angle 4.88495 ( 1989) SS BOND : bond 0.00482 ( 4) SS BOND : angle 0.55959 ( 8) covalent geometry : bond 0.00406 (10860) covalent geometry : angle 0.52752 (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 : 1.835 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: 0.7934 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: A 395 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.4827 (mm) REVERT: A 670 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.5273 (mt) REVERT: A 675 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.4143 (mpm) REVERT: A 683 MET cc_start: 0.4476 (mmt) cc_final: 0.4263 (mmt) REVERT: A 773 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.6898 (m-30) REVERT: B 158 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: B 166 TRP cc_start: 0.6719 (m100) cc_final: 0.6076 (p-90) REVERT: B 395 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.4788 (mm) REVERT: B 675 MET cc_start: 0.4550 (OUTLIER) cc_final: 0.4138 (mpm) REVERT: B 683 MET cc_start: 0.4503 (mmt) cc_final: 0.4281 (mmt) outliers start: 25 outliers final: 7 residues processed: 153 average time/residue: 1.4440 time to fit residues: 252.9251 Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 652 THR 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 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: 0.8980 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.217386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.173855 restraints weight = 31453.024| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.97 r_work: 0.3882 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1511 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= 0.132 Angle : 0.503 6.680 14760 Z= 0.273 Chirality : 0.036 0.149 1666 Planarity : 0.005 0.054 1798 Dihedral : 7.433 53.193 1508 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.16 % Allowed : 12.95 % Favored : 84.89 % 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: 1.74 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -1.11 (0.30), residues: 470 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 0.026 0.001 PHE A 598 TYR 0.019 0.001 TYR A 211 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 671) hydrogen bonds : angle 4.74304 ( 1989) SS BOND : bond 0.00416 ( 4) SS BOND : angle 0.47171 ( 8) covalent geometry : bond 0.00295 (10860) covalent geometry : angle 0.50267 (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 166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.483 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 516 PHE cc_start: 0.8283 (m-80) cc_final: 0.8031 (m-80) REVERT: A 670 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5197 (mt) REVERT: A 675 MET cc_start: 0.4431 (OUTLIER) cc_final: 0.3990 (mpm) REVERT: B 516 PHE cc_start: 0.8212 (m-80) cc_final: 0.7979 (m-80) REVERT: B 675 MET cc_start: 0.4552 (OUTLIER) cc_final: 0.4133 (mpm) outliers start: 24 outliers final: 9 residues processed: 156 average time/residue: 1.4928 time to fit residues: 266.3173 Evaluate side-chains 150 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4420 r_free = 0.4420 target = 0.218409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174727 restraints weight = 31389.548| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.00 r_work: 0.3894 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1660 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= 0.118 Angle : 0.487 6.667 14760 Z= 0.264 Chirality : 0.036 0.146 1666 Planarity : 0.004 0.054 1798 Dihedral : 7.223 50.245 1508 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 12.95 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1312 helix: 1.88 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 403 HIS 0.009 0.001 HIS A 552 PHE 0.025 0.001 PHE B 598 TYR 0.017 0.001 TYR A 211 ARG 0.001 0.000 ARG B 351 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 671) hydrogen bonds : angle 4.58826 ( 1989) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.46419 ( 8) covalent geometry : bond 0.00262 (10860) covalent geometry : angle 0.48697 (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 : 1.641 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 166 TRP cc_start: 0.6712 (m100) cc_final: 0.6035 (p-90) REVERT: A 395 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.4800 (mm) REVERT: A 516 PHE cc_start: 0.8294 (m-80) cc_final: 0.8046 (m-80) REVERT: A 670 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.5149 (mt) REVERT: A 675 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.4015 (mpm) REVERT: B 166 TRP cc_start: 0.6684 (m100) cc_final: 0.6004 (p-90) REVERT: B 395 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4772 (mm) REVERT: B 516 PHE cc_start: 0.8241 (m-80) cc_final: 0.8003 (m-80) REVERT: B 653 LEU cc_start: 0.7094 (mm) cc_final: 0.6717 (tp) REVERT: B 675 MET cc_start: 0.4492 (OUTLIER) cc_final: 0.4068 (mpm) outliers start: 23 outliers final: 6 residues processed: 157 average time/residue: 1.4700 time to fit residues: 264.2227 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 : 1.499 ------------------------------------------------------------------------------- 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 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 675 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.4403 r_free = 0.4403 target = 0.216527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.172508 restraints weight = 31638.768| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.00 r_work: 0.3855 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10864 Z= 0.160 Angle : 0.516 6.619 14760 Z= 0.279 Chirality : 0.037 0.153 1666 Planarity : 0.005 0.054 1798 Dihedral : 7.223 49.994 1508 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.80 % Allowed : 13.49 % Favored : 84.71 % 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: 1.18 (0.24), residues: 1312 helix: 1.81 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -1.15 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 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 0.002 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 671) hydrogen bonds : angle 4.65712 ( 1989) SS BOND : bond 0.00411 ( 4) SS BOND : angle 0.66178 ( 8) covalent geometry : bond 0.00367 (10860) covalent geometry : angle 0.51601 (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 162 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.492 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: 0.8274 (m-80) cc_final: 0.8041 (m-80) REVERT: A 670 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5291 (mt) REVERT: A 675 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.4009 (mpm) REVERT: A 773 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: B 516 PHE cc_start: 0.8217 (m-80) cc_final: 0.7995 (m-80) REVERT: B 555 TRP cc_start: 0.5066 (OUTLIER) cc_final: 0.4456 (m-10) REVERT: B 653 LEU cc_start: 0.7135 (mm) cc_final: 0.6769 (tp) REVERT: B 675 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.4063 (mpm) outliers start: 20 outliers final: 8 residues processed: 152 average time/residue: 1.4501 time to fit residues: 252.3312 Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 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 652 THR 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: 0.7980 chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4403 r_free = 0.4403 target = 0.216787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172445 restraints weight = 31531.880| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.99 r_work: 0.3871 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1700 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= 0.166 Angle : 0.526 6.583 14760 Z= 0.283 Chirality : 0.037 0.153 1666 Planarity : 0.005 0.053 1798 Dihedral : 7.242 49.870 1508 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.80 % Allowed : 13.94 % 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 (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: 1.10 (0.23), residues: 1312 helix: 1.75 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 403 HIS 0.006 0.001 HIS A 552 PHE 0.029 0.001 PHE A 598 TYR 0.021 0.001 TYR A 211 ARG 0.002 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 671) hydrogen bonds : angle 4.66829 ( 1989) SS BOND : bond 0.00422 ( 4) SS BOND : angle 0.65509 ( 8) covalent geometry : bond 0.00384 (10860) covalent geometry : angle 0.52596 (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 159 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.629 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 166 TRP cc_start: 0.6703 (m100) cc_final: 0.6076 (p-90) REVERT: A 516 PHE cc_start: 0.8228 (m-80) cc_final: 0.8017 (m-80) REVERT: A 555 TRP cc_start: 0.5103 (OUTLIER) cc_final: 0.4536 (m-10) REVERT: A 670 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5254 (mt) REVERT: A 675 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.4085 (mpm) REVERT: A 773 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: B 166 TRP cc_start: 0.6696 (m100) cc_final: 0.6062 (p-90) REVERT: B 269 LEU cc_start: 0.7296 (tp) cc_final: 0.7091 (mt) REVERT: B 516 PHE cc_start: 0.8228 (m-80) cc_final: 0.8026 (m-80) REVERT: B 555 TRP cc_start: 0.5096 (OUTLIER) cc_final: 0.4530 (m-10) REVERT: B 653 LEU cc_start: 0.7142 (mm) cc_final: 0.6777 (tp) REVERT: B 675 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.4101 (mpm) outliers start: 20 outliers final: 8 residues processed: 149 average time/residue: 1.4926 time to fit residues: 254.7630 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 : 1.726 ------------------------------------------------------------------------------- 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 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 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 675 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 502 GLN B 690 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.218715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174838 restraints weight = 31458.856| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.00 r_work: 0.3893 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1790 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= 0.123 Angle : 0.502 6.618 14760 Z= 0.270 Chirality : 0.036 0.146 1666 Planarity : 0.005 0.053 1798 Dihedral : 7.078 47.365 1508 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.53 % Allowed : 14.39 % Favored : 84.08 % 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: 1.29 (0.24), residues: 1312 helix: 1.90 (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 0.013 0.001 TRP A 403 HIS 0.007 0.001 HIS A 552 PHE 0.024 0.001 PHE A 598 TYR 0.018 0.001 TYR A 211 ARG 0.004 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 671) hydrogen bonds : angle 4.54892 ( 1989) SS BOND : bond 0.00359 ( 4) SS BOND : angle 0.46783 ( 8) covalent geometry : bond 0.00273 (10860) covalent geometry : angle 0.50195 (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 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.493 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 166 TRP cc_start: 0.6720 (m100) cc_final: 0.6057 (p-90) REVERT: A 395 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.4799 (mm) REVERT: A 516 PHE cc_start: 0.8263 (m-80) cc_final: 0.8056 (m-80) REVERT: A 675 MET cc_start: 0.4374 (OUTLIER) cc_final: 0.4071 (mpm) REVERT: B 166 TRP cc_start: 0.6718 (m100) cc_final: 0.6053 (p-90) REVERT: B 395 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4757 (mm) REVERT: B 516 PHE cc_start: 0.8277 (m-80) cc_final: 0.8072 (m-80) REVERT: B 555 TRP cc_start: 0.5093 (OUTLIER) cc_final: 0.4543 (m-10) REVERT: B 653 LEU cc_start: 0.7142 (mm) cc_final: 0.6781 (tp) REVERT: B 675 MET cc_start: 0.4479 (OUTLIER) cc_final: 0.4072 (mpm) outliers start: 17 outliers final: 6 residues processed: 152 average time/residue: 1.4351 time to fit residues: 251.0232 Evaluate side-chains 152 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 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 652 THR 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: 4.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 114 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4418 r_free = 0.4418 target = 0.218111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174235 restraints weight = 31538.080| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.99 r_work: 0.3887 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1845 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= 0.134 Angle : 0.508 6.617 14760 Z= 0.273 Chirality : 0.036 0.148 1666 Planarity : 0.005 0.054 1798 Dihedral : 6.959 45.515 1508 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.62 % Allowed : 14.57 % Favored : 83.81 % 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: 1.90 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 403 HIS 0.007 0.001 HIS A 552 PHE 0.027 0.001 PHE A 598 TYR 0.018 0.001 TYR A 211 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 671) hydrogen bonds : angle 4.57594 ( 1989) SS BOND : bond 0.00360 ( 4) SS BOND : angle 0.55958 ( 8) covalent geometry : bond 0.00303 (10860) covalent geometry : angle 0.50798 (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: 18 poor density : 141 time to evaluate : 1.706 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 95 ARG cc_start: 0.7050 (mmp80) cc_final: 0.6649 (mmm160) REVERT: A 166 TRP cc_start: 0.6747 (m100) cc_final: 0.6095 (p-90) REVERT: A 395 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.4825 (mm) REVERT: A 516 PHE cc_start: 0.8280 (m-80) cc_final: 0.8037 (m-80) REVERT: A 670 LEU cc_start: 0.5512 (OUTLIER) cc_final: 0.5170 (mt) REVERT: A 675 MET cc_start: 0.4391 (OUTLIER) cc_final: 0.4096 (mpm) REVERT: B 95 ARG cc_start: 0.6992 (mmp80) cc_final: 0.6553 (mmm160) REVERT: B 166 TRP cc_start: 0.6749 (m100) cc_final: 0.6098 (p-90) REVERT: B 395 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.4795 (mm) REVERT: B 516 PHE cc_start: 0.8231 (m-80) cc_final: 0.7997 (m-80) REVERT: B 555 TRP cc_start: 0.5172 (OUTLIER) cc_final: 0.4695 (m-10) REVERT: B 653 LEU cc_start: 0.7145 (mm) cc_final: 0.6800 (tp) REVERT: B 675 MET cc_start: 0.4499 (OUTLIER) cc_final: 0.4193 (mpm) outliers start: 18 outliers final: 7 residues processed: 151 average time/residue: 1.4165 time to fit residues: 246.5665 Evaluate side-chains 153 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 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 652 THR 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: 2.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.216090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.171389 restraints weight = 31648.914| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.01 r_work: 0.3855 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1858 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= 0.195 Angle : 0.554 6.505 14760 Z= 0.298 Chirality : 0.038 0.156 1666 Planarity : 0.005 0.054 1798 Dihedral : 7.138 47.392 1508 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.53 % Allowed : 14.75 % 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: 1.00 (0.24), residues: 1312 helix: 1.66 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -1.23 (0.29), residues: 468 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 0.033 0.002 PHE A 598 TYR 0.024 0.001 TYR A 211 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 671) hydrogen bonds : angle 4.74240 ( 1989) SS BOND : bond 0.00435 ( 4) SS BOND : angle 0.79389 ( 8) covalent geometry : bond 0.00455 (10860) covalent geometry : angle 0.55346 (14752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12139.84 seconds wall clock time: 208 minutes 10.99 seconds (12490.99 seconds total)