Starting phenix.real_space_refine on Fri Apr 5 23:39:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyj_26181/04_2024/7tyj_26181_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyj_26181/04_2024/7tyj_26181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyj_26181/04_2024/7tyj_26181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyj_26181/04_2024/7tyj_26181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyj_26181/04_2024/7tyj_26181_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyj_26181/04_2024/7tyj_26181_neut.pdb" } resolution = 3.3 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= 0.005 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4008 2.51 5 N 1129 2.21 5 O 1162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "B GLU 677": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6338 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3437 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 425} Chain breaks: 1 Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2901 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 23, 'TRANS': 337} Chain breaks: 3 Time building chain proxies: 3.76, per 1000 atoms: 0.59 Number of scatterers: 6338 At special positions: 0 Unit cell: (81, 85.32, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1162 8.00 N 1129 7.00 C 4008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 232 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 838 " distance=2.03 Simple disulfide: pdb=" SG CYS B 764 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 15 sheets defined 11.8% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.671A pdb=" N GLN A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 19 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.938A pdb=" N LEU A 131 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.556A pdb=" N GLY A 272 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.717A pdb=" N HIS A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.805A pdb=" N ILE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 678 through 693 removed outlier: 3.661A pdb=" N LEU B 691 " --> pdb=" O PHE B 687 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 848 removed outlier: 4.128A pdb=" N PHE B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 8.359A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 62 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 57 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE A 92 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 59 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR A 87 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG A 114 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 89 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU A 116 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 91 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.733A pdb=" N THR A 168 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 175 " --> pdb=" O THR A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.574A pdb=" N HIS A 292 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.573A pdb=" N HIS A 323 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS A 303 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 325 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A 305 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 327 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.573A pdb=" N HIS A 323 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS A 303 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 325 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A 305 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 327 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR A 415 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR A 389 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA A 417 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 391 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 459 through 460 removed outlier: 5.958A pdb=" N ARG B 459 " --> pdb=" O GLN B 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 463 through 468 removed outlier: 3.584A pdb=" N SER B 465 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AB3, first strand: chain 'B' and resid 583 through 591 removed outlier: 5.821A pdb=" N ASP B 584 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 600 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN B 590 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N HIS B 594 " --> pdb=" O ASN B 590 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 737 through 741 removed outlier: 3.782A pdb=" N GLN B 737 " --> pdb=" O TRP B 616 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP B 616 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 611 " --> pdb=" O CYS B 764 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 756 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 797 through 798 Processing sheet with id=AB6, first strand: chain 'B' and resid 835 through 840 138 hydrogen bonds defined for protein. 348 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: 1.75 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2119 1.34 - 1.46: 1485 1.46 - 1.58: 2839 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 6487 Sorted by residual: bond pdb=" CA THR A 436 " pdb=" CB THR A 436 " ideal model delta sigma weight residual 1.527 1.554 -0.027 2.48e-02 1.63e+03 1.15e+00 bond pdb=" CB LYS A 359 " pdb=" CG LYS A 359 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.95e-01 bond pdb=" CB ASP A 317 " pdb=" CG ASP A 317 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.93e-01 bond pdb=" N THR B 553 " pdb=" CA THR B 553 " ideal model delta sigma weight residual 1.460 1.471 -0.012 1.42e-02 4.96e+03 6.56e-01 bond pdb=" CG1 ILE A 127 " pdb=" CD1 ILE A 127 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 6.00e-01 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 277 107.28 - 113.96: 3589 113.96 - 120.65: 2420 120.65 - 127.33: 2445 127.33 - 134.01: 86 Bond angle restraints: 8817 Sorted by residual: angle pdb=" CA LEU B 627 " pdb=" CB LEU B 627 " pdb=" CG LEU B 627 " ideal model delta sigma weight residual 116.30 126.14 -9.84 3.50e+00 8.16e-02 7.91e+00 angle pdb=" CB MET A 381 " pdb=" CG MET A 381 " pdb=" SD MET A 381 " ideal model delta sigma weight residual 112.70 104.36 8.34 3.00e+00 1.11e-01 7.73e+00 angle pdb=" CG1 ILE A 269 " pdb=" CB ILE A 269 " pdb=" CG2 ILE A 269 " ideal model delta sigma weight residual 110.70 102.76 7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" C THR A 54 " pdb=" N ASP A 55 " pdb=" CA ASP A 55 " ideal model delta sigma weight residual 122.42 118.58 3.84 1.55e+00 4.16e-01 6.12e+00 angle pdb=" C TRP A 246 " pdb=" N ARG A 247 " pdb=" CA ARG A 247 " ideal model delta sigma weight residual 122.36 118.56 3.80 1.60e+00 3.91e-01 5.63e+00 ... (remaining 8812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 3365 18.02 - 36.05: 417 36.05 - 54.07: 100 54.07 - 72.09: 18 72.09 - 90.12: 11 Dihedral angle restraints: 3911 sinusoidal: 1580 harmonic: 2331 Sorted by residual: dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 202 " pdb=" CB CYS A 202 " ideal model delta sinusoidal sigma weight residual 93.00 -176.88 -90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 184 " pdb=" CB CYS A 184 " ideal model delta sinusoidal sigma weight residual -86.00 -161.16 75.16 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CA ARG A 10 " pdb=" C ARG A 10 " pdb=" N SER A 11 " pdb=" CA SER A 11 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 3908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 709 0.042 - 0.085: 181 0.085 - 0.127: 86 0.127 - 0.170: 5 0.170 - 0.212: 2 Chirality restraints: 983 Sorted by residual: chirality pdb=" CB ILE A 269 " pdb=" CA ILE A 269 " pdb=" CG1 ILE A 269 " pdb=" CG2 ILE A 269 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU A 226 " pdb=" CB LEU A 226 " pdb=" CD1 LEU A 226 " pdb=" CD2 LEU A 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP A 246 " pdb=" N TRP A 246 " pdb=" C TRP A 246 " pdb=" CB TRP A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 980 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 697 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 698 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 698 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 698 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 190 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 191 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 445 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ILE A 445 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE A 445 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 446 " -0.011 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 242 2.71 - 3.26: 5971 3.26 - 3.80: 9459 3.80 - 4.35: 12108 4.35 - 4.90: 21165 Nonbonded interactions: 48945 Sorted by model distance: nonbonded pdb=" OG SER B 801 " pdb=" OG SER B 805 " model vdw 2.161 2.440 nonbonded pdb=" O HIS B 766 " pdb=" OG1 THR B 770 " model vdw 2.171 2.440 nonbonded pdb=" O PRO B 856 " pdb=" OH TYR B 860 " model vdw 2.206 2.440 nonbonded pdb=" O LEU A 430 " pdb=" OG1 THR A 434 " model vdw 2.225 2.440 nonbonded pdb=" O ALA A 315 " pdb=" OG SER A 345 " model vdw 2.247 2.440 ... (remaining 48940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.720 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: 0.010 Extract box with map and model: 3.340 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 20.830 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 0.040 6487 Z= 0.269 Angle : 0.620 9.842 8817 Z= 0.317 Chirality : 0.046 0.212 983 Planarity : 0.004 0.056 1145 Dihedral : 16.632 86.456 2364 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.30 % Favored : 89.57 % Rotamer: Outliers : 0.44 % Allowed : 21.08 % Favored : 78.49 % 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: -1.90 (0.29), residues: 796 helix: 0.26 (0.70), residues: 56 sheet: -0.59 (0.38), residues: 201 loop : -1.81 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 PHE 0.012 0.002 PHE B 687 TYR 0.015 0.001 TYR A 56 ARG 0.002 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.788 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.2133 time to fit residues: 16.2978 Evaluate side-chains 58 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6487 Z= 0.160 Angle : 0.540 10.027 8817 Z= 0.275 Chirality : 0.043 0.162 983 Planarity : 0.004 0.046 1145 Dihedral : 5.111 50.106 890 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.30 % Favored : 90.58 % Rotamer: Outliers : 2.47 % Allowed : 20.06 % Favored : 77.47 % 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: -1.93 (0.29), residues: 796 helix: -0.10 (0.71), residues: 56 sheet: -0.59 (0.38), residues: 201 loop : -1.80 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.003 0.000 HIS A 123 PHE 0.009 0.001 PHE B 683 TYR 0.010 0.001 TYR A 56 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.761 Fit side-chains REVERT: A 17 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7749 (ttp-110) REVERT: A 253 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7299 (tpp80) REVERT: B 766 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.5744 (m-70) outliers start: 17 outliers final: 7 residues processed: 72 average time/residue: 0.1899 time to fit residues: 18.8339 Evaluate side-chains 66 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 766 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6487 Z= 0.168 Angle : 0.536 9.788 8817 Z= 0.271 Chirality : 0.043 0.189 983 Planarity : 0.004 0.045 1145 Dihedral : 5.009 51.381 888 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 3.49 % Allowed : 19.62 % Favored : 76.89 % 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: -1.90 (0.29), residues: 796 helix: 0.04 (0.72), residues: 56 sheet: -0.59 (0.38), residues: 201 loop : -1.77 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.003 0.000 HIS A 123 PHE 0.009 0.001 PHE B 683 TYR 0.009 0.001 TYR A 56 ARG 0.001 0.000 ARG B 645 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 0.698 Fit side-chains REVERT: A 17 ARG cc_start: 0.8030 (ttp-110) cc_final: 0.7747 (ttp-110) REVERT: A 194 MET cc_start: 0.8251 (mtp) cc_final: 0.8047 (mtp) REVERT: A 253 ARG cc_start: 0.8170 (tpp-160) cc_final: 0.7298 (tpp80) REVERT: B 766 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.5725 (m-70) outliers start: 24 outliers final: 10 residues processed: 75 average time/residue: 0.1881 time to fit residues: 19.2765 Evaluate side-chains 69 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.0010 chunk 37 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6487 Z= 0.201 Angle : 0.555 9.613 8817 Z= 0.278 Chirality : 0.043 0.201 983 Planarity : 0.004 0.044 1145 Dihedral : 4.671 31.086 886 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 3.63 % Allowed : 20.06 % Favored : 76.31 % 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: -1.91 (0.29), residues: 796 helix: 0.05 (0.72), residues: 56 sheet: -0.62 (0.38), residues: 201 loop : -1.78 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 PHE 0.010 0.001 PHE B 734 TYR 0.011 0.001 TYR B 494 ARG 0.001 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.737 Fit side-chains REVERT: A 17 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.7769 (ttp-110) REVERT: A 194 MET cc_start: 0.8274 (mtp) cc_final: 0.8062 (mtp) REVERT: A 253 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7281 (tpp80) REVERT: B 766 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.5738 (m-70) outliers start: 25 outliers final: 17 residues processed: 79 average time/residue: 0.1993 time to fit residues: 21.4866 Evaluate side-chains 75 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6487 Z= 0.437 Angle : 0.658 9.022 8817 Z= 0.332 Chirality : 0.047 0.212 983 Planarity : 0.004 0.050 1145 Dihedral : 5.338 32.690 886 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.44 % Favored : 87.44 % Rotamer: Outliers : 3.92 % Allowed : 21.51 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.29), residues: 796 helix: -0.40 (0.69), residues: 56 sheet: -1.02 (0.38), residues: 192 loop : -1.87 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 599 HIS 0.005 0.001 HIS B 762 PHE 0.014 0.002 PHE A 355 TYR 0.017 0.002 TYR B 494 ARG 0.002 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 52 time to evaluate : 0.775 Fit side-chains REVERT: A 17 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7777 (ttp-110) REVERT: A 441 ASN cc_start: 0.8381 (p0) cc_final: 0.8173 (p0) REVERT: B 506 HIS cc_start: 0.4522 (OUTLIER) cc_final: 0.4259 (t70) REVERT: B 692 HIS cc_start: 0.8095 (t70) cc_final: 0.7744 (t70) REVERT: B 766 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.5643 (m-70) outliers start: 27 outliers final: 21 residues processed: 71 average time/residue: 0.1962 time to fit residues: 19.1280 Evaluate side-chains 73 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 515 GLN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6487 Z= 0.184 Angle : 0.563 9.525 8817 Z= 0.284 Chirality : 0.044 0.190 983 Planarity : 0.004 0.048 1145 Dihedral : 4.881 29.554 886 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.67 % Favored : 91.21 % Rotamer: Outliers : 3.49 % Allowed : 22.24 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.29), residues: 796 helix: -0.29 (0.69), residues: 56 sheet: -0.74 (0.37), residues: 201 loop : -1.84 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.002 0.001 HIS A 123 PHE 0.011 0.001 PHE B 687 TYR 0.010 0.001 TYR A 56 ARG 0.001 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 51 time to evaluate : 0.764 Fit side-chains REVERT: A 17 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7781 (ttp-110) REVERT: A 253 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7262 (tpp80) REVERT: A 441 ASN cc_start: 0.8397 (p0) cc_final: 0.8162 (p0) REVERT: B 766 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.5893 (m-70) outliers start: 24 outliers final: 15 residues processed: 69 average time/residue: 0.1974 time to fit residues: 18.6717 Evaluate side-chains 67 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.0670 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6487 Z= 0.235 Angle : 0.585 9.231 8817 Z= 0.291 Chirality : 0.044 0.225 983 Planarity : 0.004 0.044 1145 Dihedral : 4.877 30.449 886 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 3.20 % Allowed : 22.67 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.29), residues: 796 helix: -0.37 (0.69), residues: 56 sheet: -0.77 (0.37), residues: 201 loop : -1.85 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 PHE 0.012 0.001 PHE B 687 TYR 0.011 0.001 TYR B 494 ARG 0.001 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 0.749 Fit side-chains REVERT: A 17 ARG cc_start: 0.8069 (ttp-110) cc_final: 0.7781 (ttp-110) REVERT: A 253 ARG cc_start: 0.8088 (tpp-160) cc_final: 0.7268 (tpp80) REVERT: A 441 ASN cc_start: 0.8371 (p0) cc_final: 0.8148 (p0) REVERT: B 692 HIS cc_start: 0.8095 (t70) cc_final: 0.7802 (t70) REVERT: B 766 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.5937 (m-70) outliers start: 22 outliers final: 20 residues processed: 70 average time/residue: 0.1991 time to fit residues: 19.0451 Evaluate side-chains 74 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6487 Z= 0.293 Angle : 0.601 9.146 8817 Z= 0.300 Chirality : 0.045 0.215 983 Planarity : 0.004 0.048 1145 Dihedral : 5.035 30.884 886 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 3.34 % Allowed : 22.67 % Favored : 73.98 % 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: -2.13 (0.29), residues: 796 helix: -0.42 (0.68), residues: 56 sheet: -0.80 (0.37), residues: 201 loop : -1.88 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 599 HIS 0.004 0.001 HIS B 762 PHE 0.012 0.002 PHE A 267 TYR 0.012 0.001 TYR B 494 ARG 0.001 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.752 Fit side-chains REVERT: A 253 ARG cc_start: 0.8118 (tpp-160) cc_final: 0.7387 (tpp80) REVERT: B 692 HIS cc_start: 0.8105 (t70) cc_final: 0.7796 (t70) REVERT: B 766 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.5844 (m-70) outliers start: 23 outliers final: 20 residues processed: 69 average time/residue: 0.2051 time to fit residues: 19.2829 Evaluate side-chains 71 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6487 Z= 0.294 Angle : 0.609 9.941 8817 Z= 0.304 Chirality : 0.045 0.230 983 Planarity : 0.004 0.047 1145 Dihedral : 5.062 30.580 886 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.06 % Favored : 88.82 % Rotamer: Outliers : 3.78 % Allowed : 21.80 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.29), residues: 796 helix: -0.47 (0.68), residues: 56 sheet: -0.86 (0.38), residues: 196 loop : -1.90 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 PHE 0.012 0.002 PHE B 687 TYR 0.012 0.001 TYR B 494 ARG 0.001 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 52 time to evaluate : 0.735 Fit side-chains REVERT: A 441 ASN cc_start: 0.8315 (p0) cc_final: 0.8044 (p0) REVERT: B 692 HIS cc_start: 0.8106 (t70) cc_final: 0.7796 (t70) REVERT: B 766 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.5845 (m-70) outliers start: 26 outliers final: 21 residues processed: 72 average time/residue: 0.1877 time to fit residues: 18.5143 Evaluate side-chains 73 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0010 chunk 52 optimal weight: 0.2980 chunk 79 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6487 Z= 0.151 Angle : 0.559 9.655 8817 Z= 0.279 Chirality : 0.043 0.203 983 Planarity : 0.004 0.044 1145 Dihedral : 4.709 29.722 886 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.92 % Favored : 90.95 % Rotamer: Outliers : 2.62 % Allowed : 22.97 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.29), residues: 796 helix: -0.28 (0.70), residues: 56 sheet: -0.72 (0.38), residues: 201 loop : -1.81 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 246 HIS 0.003 0.000 HIS A 123 PHE 0.013 0.001 PHE A 267 TYR 0.008 0.001 TYR A 56 ARG 0.002 0.000 ARG A 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.761 Fit side-chains REVERT: B 766 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.5907 (m-70) outliers start: 18 outliers final: 15 residues processed: 65 average time/residue: 0.2113 time to fit residues: 18.5609 Evaluate side-chains 67 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.140373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105528 restraints weight = 8516.502| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.66 r_work: 0.2994 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6487 Z= 0.166 Angle : 0.567 10.211 8817 Z= 0.279 Chirality : 0.044 0.236 983 Planarity : 0.004 0.045 1145 Dihedral : 4.615 30.765 886 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 3.05 % Allowed : 22.53 % Favored : 74.42 % 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: -1.98 (0.29), residues: 796 helix: -0.25 (0.69), residues: 56 sheet: -0.70 (0.38), residues: 201 loop : -1.77 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 PHE 0.012 0.001 PHE A 267 TYR 0.009 0.001 TYR B 494 ARG 0.003 0.000 ARG A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1658.21 seconds wall clock time: 30 minutes 46.40 seconds (1846.40 seconds total)