Starting phenix.real_space_refine on Mon Apr 6 14:41:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngz_49397/04_2026/9ngz_49397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngz_49397/04_2026/9ngz_49397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngz_49397/04_2026/9ngz_49397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngz_49397/04_2026/9ngz_49397.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngz_49397/04_2026/9ngz_49397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngz_49397/04_2026/9ngz_49397.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 6182 2.51 5 N 1574 2.21 5 O 1628 1.98 5 H 9626 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19024 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 9512 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 31, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 9512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 9512 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 31, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 3.04, per 1000 atoms: 0.16 Number of scatterers: 19024 At special positions: 0 Unit cell: (128.567, 77.7955, 113.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 1628 8.00 N 1574 7.00 C 6182 6.00 H 9626 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 470.4 milliseconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 68.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.703A pdb=" N TRP A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 89 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.702A pdb=" N LEU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 111 removed outlier: 3.732A pdb=" N ALA A 111 " --> pdb=" O CYS A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 111' Processing helix chain 'A' and resid 121 through 140 Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.840A pdb=" N PHE A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 175 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 200 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.618A pdb=" N LEU A 206 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 228 through 254 removed outlier: 4.161A pdb=" N PHE A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 267 removed outlier: 4.035A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 326 through 350 removed outlier: 3.634A pdb=" N GLU A 337 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 370 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.934A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 420 through 433 removed outlier: 3.605A pdb=" N LEU A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 467 through 488 Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.602A pdb=" N VAL A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 747 through 761 Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.704A pdb=" N TRP B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 89 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 93 through 107 removed outlier: 3.703A pdb=" N LEU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 111 removed outlier: 3.732A pdb=" N ALA B 111 " --> pdb=" O CYS B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 111' Processing helix chain 'B' and resid 121 through 140 Processing helix chain 'B' and resid 144 through 166 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.842A pdb=" N PHE B 174 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 175 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 200 Proline residue: B 197 - end of helix Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.619A pdb=" N LEU B 206 " --> pdb=" O GLN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 228 through 254 removed outlier: 4.160A pdb=" N PHE B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 267 removed outlier: 4.035A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B 265 " --> pdb=" O PHE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 285 Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 326 through 350 removed outlier: 3.634A pdb=" N GLU B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 370 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 380 through 390 Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.933A pdb=" N VAL B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 420 through 433 removed outlier: 3.605A pdb=" N LEU B 424 " --> pdb=" O PRO B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 467 through 488 Processing helix chain 'B' and resid 553 through 563 removed outlier: 3.605A pdb=" N VAL B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 636 Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 747 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 514 removed outlier: 5.064A pdb=" N ILE A 537 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N HIS A 745 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE A 643 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 510 through 514 removed outlier: 5.057A pdb=" N ILE B 537 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LYS B 497 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 13.665A pdb=" N VAL B 535 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE B 536 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP B 609 " --> pdb=" O PHE B 536 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE B 538 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS B 745 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE B 643 " --> pdb=" O HIS B 745 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1734 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: 3.98 Time building geometry restraints manager: 2.05 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: 9620 1.03 - 1.22: 7 1.22 - 1.42: 4039 1.42 - 1.61: 5578 1.61 - 1.81: 22 Bond restraints: 19266 Sorted by residual: bond pdb=" N ASP B 290 " pdb=" H ASP B 290 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" N ASP A 290 " pdb=" H ASP A 290 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" N ASP A 290 " pdb=" CA ASP A 290 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.14e-02 7.69e+03 2.54e+00 bond pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.14e-02 7.69e+03 2.45e+00 bond pdb=" CB GLU B 562 " pdb=" CG GLU B 562 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 ... (remaining 19261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 31771 1.23 - 2.45: 2650 2.45 - 3.68: 360 3.68 - 4.90: 90 4.90 - 6.13: 27 Bond angle restraints: 34898 Sorted by residual: angle pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " ideal model delta sigma weight residual 112.60 118.00 -5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " pdb=" CG ASP B 290 " ideal model delta sigma weight residual 112.60 117.99 -5.39 1.00e+00 1.00e+00 2.91e+01 angle pdb=" CA TYR A 254 " pdb=" CB TYR A 254 " pdb=" CG TYR A 254 " ideal model delta sigma weight residual 113.90 120.03 -6.13 1.80e+00 3.09e-01 1.16e+01 angle pdb=" CA TYR B 254 " pdb=" CB TYR B 254 " pdb=" CG TYR B 254 " ideal model delta sigma weight residual 113.90 120.02 -6.12 1.80e+00 3.09e-01 1.16e+01 angle pdb=" CA ASP A 290 " pdb=" C ASP A 290 " pdb=" O ASP A 290 " ideal model delta sigma weight residual 121.67 117.45 4.22 1.26e+00 6.30e-01 1.12e+01 ... (remaining 34893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 7944 16.73 - 33.45: 767 33.45 - 50.18: 223 50.18 - 66.90: 120 66.90 - 83.63: 6 Dihedral angle restraints: 9060 sinusoidal: 4822 harmonic: 4238 Sorted by residual: dihedral pdb=" CA GLU B 542 " pdb=" C GLU B 542 " pdb=" N SER B 543 " pdb=" CA SER B 543 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLU A 542 " pdb=" C GLU A 542 " pdb=" N SER A 543 " pdb=" CA SER A 543 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLY B 519 " pdb=" C GLY B 519 " pdb=" N GLY B 520 " pdb=" CA GLY B 520 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 9057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 943 0.031 - 0.062: 377 0.062 - 0.092: 152 0.092 - 0.123: 49 0.123 - 0.154: 21 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CB ILE B 552 " pdb=" CA ILE B 552 " pdb=" CG1 ILE B 552 " pdb=" CG2 ILE B 552 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE A 315 " pdb=" N ILE A 315 " pdb=" C ILE A 315 " pdb=" CB ILE A 315 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA VAL B 303 " pdb=" N VAL B 303 " pdb=" C VAL B 303 " pdb=" CB VAL B 303 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1539 not shown) Planarity restraints: 2782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 609 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" CG ASP B 609 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP B 609 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP B 609 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 609 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" CG ASP A 609 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP A 609 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP A 609 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 539 " -0.172 9.50e-02 1.11e+02 5.74e-02 3.67e+00 pdb=" NE ARG A 539 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 539 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 539 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 539 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 539 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 539 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 539 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 539 " -0.000 2.00e-02 2.50e+03 ... (remaining 2779 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 181 2.09 - 2.72: 32030 2.72 - 3.35: 57781 3.35 - 3.97: 72019 3.97 - 4.60: 113682 Nonbonded interactions: 275693 Sorted by model distance: nonbonded pdb="HH21 ARG B 522 " pdb="HD22 ASN B 523 " model vdw 1.463 2.100 nonbonded pdb="HH21 ARG A 522 " pdb="HD22 ASN A 523 " model vdw 1.463 2.100 nonbonded pdb="HH11 ARG A 522 " pdb=" O ASP B 510 " model vdw 1.673 2.450 nonbonded pdb=" O ASP A 510 " pdb="HH11 ARG B 522 " model vdw 1.673 2.450 nonbonded pdb=" O LEU B 273 " pdb=" HG1 THR B 277 " model vdw 1.689 2.450 ... (remaining 275688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.220 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.005 0.050 9640 Z= 0.184 Angle : 0.752 6.130 13142 Z= 0.390 Chirality : 0.043 0.154 1542 Planarity : 0.006 0.076 1634 Dihedral : 13.744 73.293 3354 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1202 helix: 1.03 (0.18), residues: 760 sheet: -1.64 (0.61), residues: 64 loop : -0.28 (0.36), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 285 TYR 0.014 0.001 TYR A 375 PHE 0.025 0.002 PHE A 200 TRP 0.018 0.002 TRP A 55 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9640) covalent geometry : angle 0.75221 (13142) hydrogen bonds : bond 0.18893 ( 594) hydrogen bonds : angle 6.76343 ( 1734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8344 (t80) cc_final: 0.7087 (m-10) REVERT: A 242 PHE cc_start: 0.7504 (t80) cc_final: 0.7233 (t80) REVERT: A 412 LEU cc_start: 0.8679 (mt) cc_final: 0.8432 (mt) REVERT: B 238 PHE cc_start: 0.8341 (t80) cc_final: 0.7078 (m-10) REVERT: B 242 PHE cc_start: 0.7495 (t80) cc_final: 0.7221 (t80) REVERT: B 412 LEU cc_start: 0.8674 (mt) cc_final: 0.8427 (mt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.6498 time to fit residues: 74.6202 Evaluate side-chains 93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN A 645 ASN B 523 ASN B 645 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.186020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152325 restraints weight = 32522.093| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.96 r_work: 0.3618 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9640 Z= 0.153 Angle : 0.542 4.756 13142 Z= 0.290 Chirality : 0.040 0.143 1542 Planarity : 0.005 0.068 1634 Dihedral : 4.235 20.299 1308 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.10 % Allowed : 15.43 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1202 helix: 1.60 (0.18), residues: 770 sheet: -1.90 (0.58), residues: 64 loop : -0.50 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.012 0.001 TYR B 95 PHE 0.021 0.002 PHE B 154 TRP 0.010 0.001 TRP A 634 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9640) covalent geometry : angle 0.54183 (13142) hydrogen bonds : bond 0.05144 ( 594) hydrogen bonds : angle 4.77905 ( 1734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8315 (t80) cc_final: 0.7071 (m-10) REVERT: A 242 PHE cc_start: 0.7463 (t80) cc_final: 0.7196 (OUTLIER) REVERT: A 652 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6613 (ttp80) REVERT: B 238 PHE cc_start: 0.8307 (t80) cc_final: 0.7063 (m-10) REVERT: B 242 PHE cc_start: 0.7470 (t80) cc_final: 0.7191 (OUTLIER) REVERT: B 652 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6602 (ttp80) outliers start: 21 outliers final: 6 residues processed: 112 average time/residue: 0.6802 time to fit residues: 85.6064 Evaluate side-chains 98 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 652 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.182766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149052 restraints weight = 32936.242| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.96 r_work: 0.3586 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9640 Z= 0.205 Angle : 0.559 5.908 13142 Z= 0.298 Chirality : 0.041 0.138 1542 Planarity : 0.005 0.037 1634 Dihedral : 4.336 20.691 1308 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.90 % Allowed : 17.43 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1202 helix: 1.36 (0.18), residues: 776 sheet: -1.81 (0.62), residues: 64 loop : -0.85 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 753 TYR 0.015 0.002 TYR B 95 PHE 0.021 0.002 PHE A 154 TRP 0.011 0.001 TRP B 634 HIS 0.005 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9640) covalent geometry : angle 0.55860 (13142) hydrogen bonds : bond 0.04754 ( 594) hydrogen bonds : angle 4.57219 ( 1734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8312 (t80) cc_final: 0.7052 (m-10) REVERT: A 242 PHE cc_start: 0.7437 (t80) cc_final: 0.7190 (t80) REVERT: A 409 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6959 (tt) REVERT: A 566 ARG cc_start: 0.5414 (tpt90) cc_final: 0.5205 (tpt90) REVERT: B 238 PHE cc_start: 0.8315 (t80) cc_final: 0.7056 (m-10) REVERT: B 242 PHE cc_start: 0.7420 (t80) cc_final: 0.7179 (t80) REVERT: B 409 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6991 (tt) REVERT: B 566 ARG cc_start: 0.5528 (tpt90) cc_final: 0.5318 (tpt90) outliers start: 19 outliers final: 11 residues processed: 112 average time/residue: 0.7666 time to fit residues: 95.9405 Evaluate side-chains 107 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.184063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150712 restraints weight = 32717.278| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.96 r_work: 0.3597 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9640 Z= 0.146 Angle : 0.511 5.048 13142 Z= 0.268 Chirality : 0.039 0.140 1542 Planarity : 0.005 0.036 1634 Dihedral : 4.225 19.892 1308 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.20 % Allowed : 18.04 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.25), residues: 1202 helix: 1.57 (0.19), residues: 774 sheet: -1.71 (0.63), residues: 64 loop : -0.67 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 753 TYR 0.013 0.001 TYR A 95 PHE 0.016 0.001 PHE B 154 TRP 0.010 0.001 TRP A 634 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9640) covalent geometry : angle 0.51051 (13142) hydrogen bonds : bond 0.04056 ( 594) hydrogen bonds : angle 4.39010 ( 1734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8323 (t80) cc_final: 0.7085 (m-10) REVERT: A 242 PHE cc_start: 0.7467 (t80) cc_final: 0.7227 (t80) REVERT: A 566 ARG cc_start: 0.5343 (tpt90) cc_final: 0.5091 (tpt90) REVERT: B 238 PHE cc_start: 0.8324 (t80) cc_final: 0.7072 (m-10) REVERT: B 242 PHE cc_start: 0.7451 (t80) cc_final: 0.7209 (t80) REVERT: B 566 ARG cc_start: 0.5390 (tpt90) cc_final: 0.5127 (tpt90) outliers start: 22 outliers final: 14 residues processed: 105 average time/residue: 0.7918 time to fit residues: 92.3729 Evaluate side-chains 103 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 501 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149649 restraints weight = 32748.740| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.96 r_work: 0.3589 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9640 Z= 0.165 Angle : 0.518 4.798 13142 Z= 0.273 Chirality : 0.039 0.137 1542 Planarity : 0.005 0.038 1634 Dihedral : 4.263 19.362 1308 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.10 % Allowed : 18.04 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1202 helix: 1.48 (0.18), residues: 778 sheet: -1.67 (0.64), residues: 64 loop : -0.79 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 285 TYR 0.014 0.001 TYR B 95 PHE 0.018 0.001 PHE B 154 TRP 0.010 0.001 TRP A 634 HIS 0.008 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9640) covalent geometry : angle 0.51779 (13142) hydrogen bonds : bond 0.04105 ( 594) hydrogen bonds : angle 4.38034 ( 1734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8311 (t80) cc_final: 0.7067 (m-10) REVERT: A 242 PHE cc_start: 0.7448 (t80) cc_final: 0.7207 (t80) REVERT: A 409 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6853 (tt) REVERT: A 566 ARG cc_start: 0.5383 (tpt90) cc_final: 0.5152 (tpt90) REVERT: B 238 PHE cc_start: 0.8315 (t80) cc_final: 0.7056 (m-10) REVERT: B 242 PHE cc_start: 0.7443 (t80) cc_final: 0.7198 (t80) REVERT: B 409 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6832 (tt) REVERT: B 566 ARG cc_start: 0.5454 (tpt90) cc_final: 0.5220 (tpt90) outliers start: 21 outliers final: 17 residues processed: 101 average time/residue: 0.7721 time to fit residues: 86.8346 Evaluate side-chains 106 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 526 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.183661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150179 restraints weight = 32509.070| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.94 r_work: 0.3597 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9640 Z= 0.145 Angle : 0.514 6.425 13142 Z= 0.268 Chirality : 0.039 0.139 1542 Planarity : 0.005 0.037 1634 Dihedral : 4.198 18.906 1308 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.71 % Allowed : 17.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1202 helix: 1.57 (0.19), residues: 776 sheet: -1.63 (0.64), residues: 64 loop : -0.80 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.013 0.001 TYR A 95 PHE 0.016 0.001 PHE B 154 TRP 0.009 0.001 TRP A 634 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9640) covalent geometry : angle 0.51355 (13142) hydrogen bonds : bond 0.03931 ( 594) hydrogen bonds : angle 4.31986 ( 1734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8322 (t80) cc_final: 0.7066 (m-10) REVERT: A 409 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6813 (tt) REVERT: A 566 ARG cc_start: 0.5339 (tpt90) cc_final: 0.5110 (tpt90) REVERT: B 238 PHE cc_start: 0.8320 (t80) cc_final: 0.7047 (m-10) REVERT: B 566 ARG cc_start: 0.5390 (tpt90) cc_final: 0.5140 (tpt90) outliers start: 27 outliers final: 18 residues processed: 104 average time/residue: 0.6799 time to fit residues: 80.0855 Evaluate side-chains 105 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 526 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 105 optimal weight: 0.0570 chunk 84 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151679 restraints weight = 32716.365| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.95 r_work: 0.3610 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9640 Z= 0.114 Angle : 0.497 7.437 13142 Z= 0.257 Chirality : 0.039 0.184 1542 Planarity : 0.004 0.035 1634 Dihedral : 4.081 18.312 1308 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.40 % Allowed : 17.74 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1202 helix: 1.79 (0.19), residues: 776 sheet: -1.64 (0.64), residues: 64 loop : -0.71 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 753 TYR 0.011 0.001 TYR B 95 PHE 0.012 0.001 PHE A 544 TRP 0.008 0.001 TRP B 634 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9640) covalent geometry : angle 0.49669 (13142) hydrogen bonds : bond 0.03667 ( 594) hydrogen bonds : angle 4.22931 ( 1734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8316 (t80) cc_final: 0.7107 (m-10) REVERT: A 242 PHE cc_start: 0.7636 (t80) cc_final: 0.7325 (t80) REVERT: B 238 PHE cc_start: 0.8326 (t80) cc_final: 0.7089 (m-10) REVERT: B 242 PHE cc_start: 0.7648 (t80) cc_final: 0.7334 (t80) REVERT: B 566 ARG cc_start: 0.5342 (tpt90) cc_final: 0.4712 (ttp80) outliers start: 24 outliers final: 17 residues processed: 103 average time/residue: 0.7045 time to fit residues: 81.6935 Evaluate side-chains 100 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 526 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS B 525 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.183605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150310 restraints weight = 32722.145| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.94 r_work: 0.3598 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9640 Z= 0.141 Angle : 0.511 7.689 13142 Z= 0.267 Chirality : 0.040 0.202 1542 Planarity : 0.004 0.037 1634 Dihedral : 4.111 18.048 1308 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.00 % Allowed : 18.24 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1202 helix: 1.75 (0.19), residues: 776 sheet: -1.61 (0.64), residues: 64 loop : -0.79 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.012 0.001 TYR B 95 PHE 0.015 0.001 PHE B 154 TRP 0.009 0.001 TRP B 634 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9640) covalent geometry : angle 0.51132 (13142) hydrogen bonds : bond 0.03771 ( 594) hydrogen bonds : angle 4.21704 ( 1734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8346 (t80) cc_final: 0.7108 (m-10) REVERT: A 242 PHE cc_start: 0.7663 (t80) cc_final: 0.7362 (t80) REVERT: A 566 ARG cc_start: 0.4770 (tpt90) cc_final: 0.4114 (ttp80) REVERT: B 76 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7908 (mp) REVERT: B 238 PHE cc_start: 0.8346 (t80) cc_final: 0.7092 (m-10) REVERT: B 242 PHE cc_start: 0.7670 (t80) cc_final: 0.7365 (t80) outliers start: 20 outliers final: 18 residues processed: 100 average time/residue: 0.7226 time to fit residues: 81.1721 Evaluate side-chains 104 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 526 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.183056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149720 restraints weight = 32748.631| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.95 r_work: 0.3591 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9640 Z= 0.152 Angle : 0.516 7.537 13142 Z= 0.271 Chirality : 0.039 0.170 1542 Planarity : 0.004 0.038 1634 Dihedral : 4.137 18.395 1308 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.51 % Allowed : 17.74 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1202 helix: 1.71 (0.19), residues: 776 sheet: -1.58 (0.64), residues: 64 loop : -0.82 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.013 0.001 TYR B 95 PHE 0.015 0.001 PHE B 154 TRP 0.009 0.001 TRP A 634 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9640) covalent geometry : angle 0.51637 (13142) hydrogen bonds : bond 0.03842 ( 594) hydrogen bonds : angle 4.23200 ( 1734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 238 PHE cc_start: 0.8328 (t80) cc_final: 0.7074 (m-10) REVERT: A 566 ARG cc_start: 0.4855 (tpt90) cc_final: 0.4290 (ttp80) REVERT: B 76 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 238 PHE cc_start: 0.8331 (t80) cc_final: 0.7058 (m-10) REVERT: B 566 ARG cc_start: 0.4891 (tpt90) cc_final: 0.4305 (ttp80) outliers start: 25 outliers final: 18 residues processed: 103 average time/residue: 0.6968 time to fit residues: 81.0309 Evaluate side-chains 106 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 526 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.182831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149551 restraints weight = 32789.614| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.95 r_work: 0.3588 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9640 Z= 0.152 Angle : 0.515 7.782 13142 Z= 0.270 Chirality : 0.040 0.206 1542 Planarity : 0.004 0.039 1634 Dihedral : 4.137 18.342 1308 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.51 % Allowed : 17.74 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1202 helix: 1.71 (0.19), residues: 776 sheet: -1.54 (0.65), residues: 64 loop : -0.84 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 566 TYR 0.013 0.001 TYR B 95 PHE 0.015 0.001 PHE A 154 TRP 0.009 0.001 TRP B 634 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9640) covalent geometry : angle 0.51515 (13142) hydrogen bonds : bond 0.03831 ( 594) hydrogen bonds : angle 4.22823 ( 1734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue LYS 308 is missing expected H atoms. Skipping. Residue LYS 664 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8334 (t80) cc_final: 0.7075 (m-10) REVERT: A 242 PHE cc_start: 0.7702 (t80) cc_final: 0.6835 (t80) REVERT: A 566 ARG cc_start: 0.4790 (tpt90) cc_final: 0.4247 (ttp80) REVERT: B 76 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 238 PHE cc_start: 0.8334 (t80) cc_final: 0.7054 (m-10) REVERT: B 242 PHE cc_start: 0.7696 (t80) cc_final: 0.6826 (t80) REVERT: B 566 ARG cc_start: 0.4907 (tpt90) cc_final: 0.4300 (ttp-170) outliers start: 25 outliers final: 19 residues processed: 101 average time/residue: 0.6745 time to fit residues: 76.5907 Evaluate side-chains 104 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 526 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.183423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150382 restraints weight = 32719.263| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.93 r_work: 0.3597 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9640 Z= 0.132 Angle : 0.508 8.507 13142 Z= 0.264 Chirality : 0.040 0.246 1542 Planarity : 0.004 0.037 1634 Dihedral : 4.099 17.938 1308 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.10 % Allowed : 18.24 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1202 helix: 1.79 (0.19), residues: 776 sheet: -1.51 (0.65), residues: 64 loop : -0.80 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 566 TYR 0.012 0.001 TYR B 95 PHE 0.017 0.001 PHE B 154 TRP 0.009 0.001 TRP B 634 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9640) covalent geometry : angle 0.50814 (13142) hydrogen bonds : bond 0.03703 ( 594) hydrogen bonds : angle 4.19035 ( 1734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5575.31 seconds wall clock time: 95 minutes 6.94 seconds (5706.94 seconds total)