Starting phenix.real_space_refine on Wed Feb 4 10:10:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lws_63458/02_2026/9lws_63458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lws_63458/02_2026/9lws_63458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lws_63458/02_2026/9lws_63458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lws_63458/02_2026/9lws_63458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lws_63458/02_2026/9lws_63458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lws_63458/02_2026/9lws_63458.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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 68 5.16 5 C 6278 2.51 5 N 1704 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9848 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7840 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 926} Chain breaks: 5 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2008 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 239} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 2.61, per 1000 atoms: 0.27 Number of scatterers: 9848 At special positions: 0 Unit cell: (86.751, 132.804, 106.029, 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 68 16.00 O 1798 8.00 N 1704 7.00 C 6278 6.00 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: 0.80 Conformation dependent library (CDL) restraints added in 477.2 milliseconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 50.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.815A pdb=" N LYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.549A pdb=" N ARG A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 124 through 131 removed outlier: 4.214A pdb=" N PHE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 4.089A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.654A pdb=" N ARG A 309 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 560 through 563 removed outlier: 6.221A pdb=" N GLU A 563 " --> pdb=" O THR A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 564 through 572 removed outlier: 4.062A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.824A pdb=" N ALA A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 631 through 640 removed outlier: 4.115A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.593A pdb=" N ARG A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.695A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.460A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.912A pdb=" N LEU A 793 " --> pdb=" O MET A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.644A pdb=" N MET A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 888 through 911 removed outlier: 4.288A pdb=" N ALA A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 974 through 994 removed outlier: 3.746A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.686A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1014 removed outlier: 4.406A pdb=" N GLN A1014 " --> pdb=" O PRO A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1025 Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.777A pdb=" N ARG A1047 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 442 through 509 Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 523 through 582 Proline residue: B 568 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 7.055A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212 removed outlier: 8.400A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ALA A 289 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.150A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.684A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 439 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.926A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA7, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AA8, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA9, first strand: chain 'B' and resid 377 through 382 removed outlier: 4.453A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 384 through 386 496 hydrogen bonds defined for protein. 1437 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: 1.68 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1647 1.31 - 1.43: 2602 1.43 - 1.56: 5696 1.56 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 10052 Sorted by residual: bond pdb=" C PRO A 471 " pdb=" O PRO A 471 " ideal model delta sigma weight residual 1.233 1.183 0.051 1.23e-02 6.61e+03 1.69e+01 bond pdb=" C THR A 470 " pdb=" N PRO A 471 " ideal model delta sigma weight residual 1.331 1.367 -0.036 1.20e-02 6.94e+03 9.04e+00 bond pdb=" N ARG B 340 " pdb=" CA ARG B 340 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.83e+00 bond pdb=" N GLN B 501 " pdb=" CA GLN B 501 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.31e+00 bond pdb=" N ASN A 497 " pdb=" CA ASN A 497 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.90e+00 ... (remaining 10047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 13292 2.09 - 4.18: 251 4.18 - 6.26: 25 6.26 - 8.35: 3 8.35 - 10.44: 5 Bond angle restraints: 13576 Sorted by residual: angle pdb=" C PRO A 471 " pdb=" CA PRO A 471 " pdb=" CB PRO A 471 " ideal model delta sigma weight residual 111.64 101.70 9.94 1.26e+00 6.30e-01 6.22e+01 angle pdb=" N ALA A1046 " pdb=" CA ALA A1046 " pdb=" C ALA A1046 " ideal model delta sigma weight residual 110.80 119.82 -9.02 2.13e+00 2.20e-01 1.80e+01 angle pdb=" N ARG B 340 " pdb=" CA ARG B 340 " pdb=" C ARG B 340 " ideal model delta sigma weight residual 110.80 119.16 -8.36 2.13e+00 2.20e-01 1.54e+01 angle pdb=" CA GLU B 496 " pdb=" CB GLU B 496 " pdb=" CG GLU B 496 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA LEU A 475 " pdb=" C LEU A 475 " pdb=" O LEU A 475 " ideal model delta sigma weight residual 121.49 117.41 4.08 1.16e+00 7.43e-01 1.24e+01 ... (remaining 13571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 5419 16.72 - 33.43: 550 33.43 - 50.15: 129 50.15 - 66.86: 22 66.86 - 83.58: 13 Dihedral angle restraints: 6133 sinusoidal: 2547 harmonic: 3586 Sorted by residual: dihedral pdb=" CD ARG B 503 " pdb=" NE ARG B 503 " pdb=" CZ ARG B 503 " pdb=" NH1 ARG B 503 " ideal model delta sinusoidal sigma weight residual 0.00 82.17 -82.17 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" N HIS A1048 " pdb=" C HIS A1048 " pdb=" CA HIS A1048 " pdb=" CB HIS A1048 " ideal model delta harmonic sigma weight residual 122.80 135.69 -12.89 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" C HIS A1048 " pdb=" N HIS A1048 " pdb=" CA HIS A1048 " pdb=" CB HIS A1048 " ideal model delta harmonic sigma weight residual -122.60 -134.89 12.29 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 6130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1406 0.092 - 0.184: 77 0.184 - 0.276: 4 0.276 - 0.368: 2 0.368 - 0.460: 1 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA HIS A1048 " pdb=" N HIS A1048 " pdb=" C HIS A1048 " pdb=" CB HIS A1048 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CA ARG B 340 " pdb=" N ARG B 340 " pdb=" C ARG B 340 " pdb=" CB ARG B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA LEU A 475 " pdb=" N LEU A 475 " pdb=" C LEU A 475 " pdb=" CB LEU A 475 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1487 not shown) Planarity restraints: 1744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 503 " 1.092 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG B 503 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 503 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 503 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 503 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 230 " 0.195 9.50e-02 1.11e+02 8.76e-02 4.71e+00 pdb=" NE ARG A 230 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 230 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 230 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 230 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 496 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" CD GLU B 496 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 496 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 496 " 0.011 2.00e-02 2.50e+03 ... (remaining 1741 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 191 2.69 - 3.24: 9782 3.24 - 3.79: 15937 3.79 - 4.35: 20831 4.35 - 4.90: 34254 Nonbonded interactions: 80995 Sorted by model distance: nonbonded pdb=" OH TYR A 988 " pdb=" O THR A1025 " model vdw 2.135 3.040 nonbonded pdb=" NE2 GLN A 809 " pdb=" OE1 GLU A1012 " model vdw 2.177 3.120 nonbonded pdb=" OD1 ASP B 529 " pdb=" NZ LYS B 532 " model vdw 2.185 3.120 nonbonded pdb=" OH TYR A 584 " pdb=" OD1 ASP A 608 " model vdw 2.218 3.040 nonbonded pdb=" NH1 ARG A 398 " pdb=" OH TYR A 644 " model vdw 2.221 3.120 ... (remaining 80990 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: 0.00 ========== 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: 1.300 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 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 0.051 10052 Z= 0.213 Angle : 0.694 10.440 13576 Z= 0.398 Chirality : 0.048 0.460 1490 Planarity : 0.013 0.489 1744 Dihedral : 14.682 83.576 3801 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.10 % Favored : 94.32 % Rotamer: Outliers : 0.94 % Allowed : 1.12 % Favored : 97.94 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.17 % 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: 0.21 (0.25), residues: 1197 helix: 1.08 (0.22), residues: 576 sheet: -1.28 (0.43), residues: 133 loop : -0.47 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 335 TYR 0.027 0.002 TYR B 580 PHE 0.014 0.002 PHE A 751 TRP 0.014 0.002 TRP A 780 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00413 (10052) covalent geometry : angle 0.69360 (13576) hydrogen bonds : bond 0.13285 ( 496) hydrogen bonds : angle 5.65492 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.5728 (ptp) cc_final: 0.5501 (mtm) REVERT: A 282 MET cc_start: 0.6241 (tpp) cc_final: 0.5909 (tpp) REVERT: A 820 MET cc_start: 0.7551 (mtt) cc_final: 0.7304 (mtt) outliers start: 10 outliers final: 2 residues processed: 144 average time/residue: 0.6638 time to fit residues: 101.8057 Evaluate side-chains 108 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 471 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 219 GLN A 450 HIS ** A 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS A 809 GLN B 410 ASN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.231655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.179658 restraints weight = 8530.507| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 1.91 r_work: 0.3987 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10052 Z= 0.303 Angle : 0.806 9.555 13576 Z= 0.415 Chirality : 0.049 0.231 1490 Planarity : 0.006 0.058 1744 Dihedral : 5.396 43.641 1330 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % Rotamer: Outliers : 2.06 % Allowed : 13.00 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.47 (0.24), residues: 1197 helix: 0.55 (0.21), residues: 580 sheet: -1.12 (0.42), residues: 141 loop : -1.03 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 401 TYR 0.033 0.003 TYR A 307 PHE 0.022 0.003 PHE A 897 TRP 0.020 0.003 TRP A 552 HIS 0.008 0.002 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00729 (10052) covalent geometry : angle 0.80572 (13576) hydrogen bonds : bond 0.05745 ( 496) hydrogen bonds : angle 5.14931 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 282 MET cc_start: 0.6271 (tpp) cc_final: 0.5722 (tpp) REVERT: A 820 MET cc_start: 0.7441 (mtt) cc_final: 0.7025 (mtt) REVERT: A 821 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6226 (tt0) REVERT: A 1038 TYR cc_start: 0.6370 (t80) cc_final: 0.6090 (t80) REVERT: B 499 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7498 (tm-30) outliers start: 22 outliers final: 6 residues processed: 145 average time/residue: 0.6049 time to fit residues: 94.0342 Evaluate side-chains 118 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 821 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 62 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.236628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.185137 restraints weight = 8404.888| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 1.71 r_work: 0.4081 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10052 Z= 0.144 Angle : 0.601 8.389 13576 Z= 0.311 Chirality : 0.041 0.150 1490 Planarity : 0.004 0.047 1744 Dihedral : 4.576 20.618 1327 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.85 % Favored : 94.99 % Rotamer: Outliers : 2.06 % Allowed : 17.59 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.31 (0.25), residues: 1197 helix: 1.28 (0.22), residues: 583 sheet: -1.13 (0.43), residues: 135 loop : -0.64 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 562 TYR 0.017 0.001 TYR A 392 PHE 0.012 0.001 PHE A 751 TRP 0.013 0.002 TRP A 552 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00329 (10052) covalent geometry : angle 0.60083 (13576) hydrogen bonds : bond 0.04313 ( 496) hydrogen bonds : angle 4.55034 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.6200 (tpp) cc_final: 0.5899 (tpp) REVERT: A 353 LYS cc_start: 0.7817 (mttm) cc_final: 0.7552 (ttmt) REVERT: A 375 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6734 (mpt180) REVERT: A 589 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: A 767 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7038 (mp0) REVERT: A 821 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5961 (tt0) REVERT: B 499 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7433 (tm-30) REVERT: B 502 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7861 (pp20) REVERT: B 509 ILE cc_start: 0.2491 (OUTLIER) cc_final: 0.2263 (pp) outliers start: 22 outliers final: 6 residues processed: 134 average time/residue: 0.5787 time to fit residues: 83.3609 Evaluate side-chains 121 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 509 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.238467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.187497 restraints weight = 8474.449| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 1.78 r_work: 0.4088 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10052 Z= 0.134 Angle : 0.579 8.179 13576 Z= 0.300 Chirality : 0.040 0.159 1490 Planarity : 0.004 0.050 1744 Dihedral : 4.394 21.031 1325 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.68 % Favored : 95.15 % Rotamer: Outliers : 2.15 % Allowed : 18.43 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.57 (0.25), residues: 1197 helix: 1.57 (0.22), residues: 585 sheet: -0.95 (0.45), residues: 136 loop : -0.65 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 562 TYR 0.018 0.001 TYR A 432 PHE 0.015 0.002 PHE A1039 TRP 0.013 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00306 (10052) covalent geometry : angle 0.57853 (13576) hydrogen bonds : bond 0.04063 ( 496) hydrogen bonds : angle 4.36931 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.5557 (tpt) cc_final: 0.4356 (pp-130) REVERT: A 282 MET cc_start: 0.6104 (tpp) cc_final: 0.5712 (tpp) REVERT: A 353 LYS cc_start: 0.7854 (mttm) cc_final: 0.7591 (ttmt) REVERT: A 375 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6705 (mpt180) REVERT: A 767 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7005 (mp0) REVERT: B 499 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 502 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7932 (pp20) outliers start: 23 outliers final: 10 residues processed: 133 average time/residue: 0.5328 time to fit residues: 76.2999 Evaluate side-chains 119 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 119 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.239659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.188931 restraints weight = 8410.561| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 1.81 r_work: 0.4090 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10052 Z= 0.127 Angle : 0.570 9.336 13576 Z= 0.291 Chirality : 0.039 0.144 1490 Planarity : 0.004 0.050 1744 Dihedral : 4.268 20.873 1325 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 2.99 % Allowed : 18.62 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.71 (0.25), residues: 1197 helix: 1.73 (0.22), residues: 585 sheet: -0.96 (0.44), residues: 136 loop : -0.63 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 562 TYR 0.018 0.001 TYR A 432 PHE 0.022 0.002 PHE A1039 TRP 0.013 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00289 (10052) covalent geometry : angle 0.56985 (13576) hydrogen bonds : bond 0.03917 ( 496) hydrogen bonds : angle 4.25041 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.5273 (tpt) cc_final: 0.4342 (pp-130) REVERT: A 278 MET cc_start: 0.7203 (ttp) cc_final: 0.6974 (ttp) REVERT: A 282 MET cc_start: 0.6107 (tpp) cc_final: 0.5621 (tpp) REVERT: A 353 LYS cc_start: 0.7895 (mttm) cc_final: 0.7644 (ttmt) REVERT: A 375 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6688 (mpt180) REVERT: A 469 GLU cc_start: 0.6197 (tp30) cc_final: 0.5410 (tm-30) REVERT: A 767 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6956 (mp0) REVERT: A 772 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.2821 (mpt) REVERT: A 956 LEU cc_start: 0.4875 (OUTLIER) cc_final: 0.4594 (mt) REVERT: A 1005 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.5825 (mmt) REVERT: A 1039 PHE cc_start: 0.4626 (t80) cc_final: 0.4362 (t80) REVERT: B 499 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 502 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7924 (pp20) outliers start: 32 outliers final: 15 residues processed: 134 average time/residue: 0.4671 time to fit residues: 68.1188 Evaluate side-chains 125 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.233193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.182321 restraints weight = 8552.328| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.97 r_work: 0.4002 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10052 Z= 0.213 Angle : 0.663 9.297 13576 Z= 0.338 Chirality : 0.043 0.180 1490 Planarity : 0.005 0.049 1744 Dihedral : 4.636 20.538 1325 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 3.55 % Allowed : 20.39 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.29 (0.25), residues: 1197 helix: 1.32 (0.22), residues: 578 sheet: -0.87 (0.45), residues: 131 loop : -0.83 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 401 TYR 0.025 0.002 TYR A 307 PHE 0.015 0.002 PHE A1016 TRP 0.013 0.002 TRP A 552 HIS 0.005 0.001 HIS A 878 Details of bonding type rmsd covalent geometry : bond 0.00507 (10052) covalent geometry : angle 0.66294 (13576) hydrogen bonds : bond 0.04661 ( 496) hydrogen bonds : angle 4.61067 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.4871 (tpt) cc_final: 0.4053 (pp-130) REVERT: A 282 MET cc_start: 0.6160 (tpp) cc_final: 0.5640 (tpp) REVERT: A 353 LYS cc_start: 0.7930 (mttm) cc_final: 0.7628 (ttmt) REVERT: A 375 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6714 (mpt90) REVERT: A 380 ASN cc_start: 0.8022 (t0) cc_final: 0.7713 (t0) REVERT: A 589 ASP cc_start: 0.7444 (m-30) cc_final: 0.7168 (m-30) REVERT: A 674 GLU cc_start: 0.5527 (OUTLIER) cc_final: 0.5282 (mm-30) REVERT: A 767 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6977 (mp0) REVERT: B 499 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 502 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8092 (pp20) outliers start: 38 outliers final: 17 residues processed: 143 average time/residue: 0.4682 time to fit residues: 72.6777 Evaluate side-chains 129 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1040 MET Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 103 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 384 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.239360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.185859 restraints weight = 8612.528| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 1.91 r_work: 0.4091 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10052 Z= 0.139 Angle : 0.603 10.148 13576 Z= 0.309 Chirality : 0.040 0.207 1490 Planarity : 0.004 0.042 1744 Dihedral : 4.389 21.076 1325 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 2.99 % Allowed : 21.80 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.57 (0.25), residues: 1197 helix: 1.64 (0.22), residues: 582 sheet: -0.94 (0.45), residues: 134 loop : -0.77 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 562 TYR 0.024 0.002 TYR A 432 PHE 0.014 0.002 PHE A1039 TRP 0.015 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00325 (10052) covalent geometry : angle 0.60327 (13576) hydrogen bonds : bond 0.03984 ( 496) hydrogen bonds : angle 4.37573 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.5870 (mmm) REVERT: A 232 MET cc_start: 0.5121 (tpt) cc_final: 0.4399 (pp-130) REVERT: A 282 MET cc_start: 0.6182 (tpp) cc_final: 0.5583 (tpp) REVERT: A 353 LYS cc_start: 0.7960 (mttm) cc_final: 0.7697 (ttmt) REVERT: A 375 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6772 (mpt90) REVERT: A 380 ASN cc_start: 0.8035 (t0) cc_final: 0.7699 (t0) REVERT: A 469 GLU cc_start: 0.6234 (tp30) cc_final: 0.5440 (tm-30) REVERT: A 767 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6951 (mp0) REVERT: A 956 LEU cc_start: 0.4608 (OUTLIER) cc_final: 0.3882 (tp) REVERT: B 499 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7357 (tm-30) REVERT: B 502 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8008 (pp20) outliers start: 32 outliers final: 17 residues processed: 137 average time/residue: 0.4895 time to fit residues: 73.0748 Evaluate side-chains 126 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.236021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.186340 restraints weight = 8520.542| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 1.84 r_work: 0.4058 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10052 Z= 0.202 Angle : 0.682 10.268 13576 Z= 0.349 Chirality : 0.044 0.201 1490 Planarity : 0.005 0.045 1744 Dihedral : 4.631 20.964 1325 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 3.18 % Allowed : 22.17 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.22 (0.25), residues: 1197 helix: 1.32 (0.22), residues: 580 sheet: -0.97 (0.45), residues: 132 loop : -0.93 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 401 TYR 0.024 0.002 TYR A 988 PHE 0.026 0.002 PHE A1039 TRP 0.012 0.002 TRP A 552 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00485 (10052) covalent geometry : angle 0.68192 (13576) hydrogen bonds : bond 0.04564 ( 496) hydrogen bonds : angle 4.62311 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.6024 (pp) cc_final: 0.5798 (mt) REVERT: A 164 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.5965 (mmm) REVERT: A 232 MET cc_start: 0.5064 (tpt) cc_final: 0.4377 (pp-130) REVERT: A 282 MET cc_start: 0.6227 (tpp) cc_final: 0.5672 (tpp) REVERT: A 353 LYS cc_start: 0.7965 (mttm) cc_final: 0.7764 (ttmt) REVERT: A 375 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6778 (mpt90) REVERT: A 380 ASN cc_start: 0.8047 (t0) cc_final: 0.7746 (t0) REVERT: A 469 GLU cc_start: 0.6069 (tp30) cc_final: 0.5343 (tm-30) REVERT: A 674 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.5275 (mm-30) REVERT: A 767 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7106 (mp0) REVERT: B 499 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7371 (tm-30) outliers start: 34 outliers final: 19 residues processed: 141 average time/residue: 0.4622 time to fit residues: 70.4187 Evaluate side-chains 126 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 509 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 384 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.240101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.186802 restraints weight = 8498.003| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 1.97 r_work: 0.4072 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10052 Z= 0.149 Angle : 0.649 15.192 13576 Z= 0.327 Chirality : 0.041 0.156 1490 Planarity : 0.004 0.045 1744 Dihedral : 4.442 21.030 1325 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 2.53 % Allowed : 23.20 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.47 (0.25), residues: 1197 helix: 1.53 (0.22), residues: 582 sheet: -1.04 (0.45), residues: 133 loop : -0.77 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 461 TYR 0.030 0.002 TYR A 988 PHE 0.015 0.002 PHE A1016 TRP 0.015 0.002 TRP A 780 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00349 (10052) covalent geometry : angle 0.64870 (13576) hydrogen bonds : bond 0.04103 ( 496) hydrogen bonds : angle 4.43515 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.5947 (mmm) REVERT: A 232 MET cc_start: 0.5099 (tpt) cc_final: 0.4398 (pp-130) REVERT: A 282 MET cc_start: 0.6178 (tpp) cc_final: 0.5722 (tpp) REVERT: A 353 LYS cc_start: 0.8001 (mttm) cc_final: 0.7799 (ttmt) REVERT: A 375 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6742 (mpt90) REVERT: A 380 ASN cc_start: 0.7960 (t0) cc_final: 0.7654 (t0) REVERT: A 469 GLU cc_start: 0.6093 (tp30) cc_final: 0.5424 (tm-30) REVERT: A 674 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.5226 (mm-30) REVERT: A 767 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7109 (mp0) outliers start: 27 outliers final: 19 residues processed: 131 average time/residue: 0.4979 time to fit residues: 70.4227 Evaluate side-chains 128 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain A residue 1040 MET Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 0.0470 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 0.1980 chunk 33 optimal weight: 0.0870 chunk 97 optimal weight: 0.0170 chunk 105 optimal weight: 3.9990 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 HIS B 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.245979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.192396 restraints weight = 8381.231| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 1.82 r_work: 0.4168 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10052 Z= 0.114 Angle : 0.612 15.331 13576 Z= 0.308 Chirality : 0.039 0.218 1490 Planarity : 0.004 0.042 1744 Dihedral : 4.080 22.084 1325 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 2.15 % Allowed : 23.67 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.84 (0.25), residues: 1197 helix: 1.86 (0.22), residues: 585 sheet: -0.95 (0.45), residues: 134 loop : -0.59 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 461 TYR 0.024 0.001 TYR A 904 PHE 0.015 0.001 PHE A1016 TRP 0.016 0.001 TRP A 780 HIS 0.004 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00257 (10052) covalent geometry : angle 0.61154 (13576) hydrogen bonds : bond 0.03560 ( 496) hydrogen bonds : angle 4.13520 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.4813 (tpt) cc_final: 0.4186 (pp-130) REVERT: A 278 MET cc_start: 0.6958 (ttp) cc_final: 0.6734 (ttp) REVERT: A 282 MET cc_start: 0.6121 (tpp) cc_final: 0.5735 (tpp) REVERT: A 353 LYS cc_start: 0.7915 (mttm) cc_final: 0.7646 (ttmt) REVERT: A 380 ASN cc_start: 0.7976 (t0) cc_final: 0.7667 (t0) REVERT: A 469 GLU cc_start: 0.5868 (tp30) cc_final: 0.5196 (tm-30) REVERT: A 675 MET cc_start: 0.6796 (tpt) cc_final: 0.6282 (mmt) REVERT: A 745 MET cc_start: 0.6351 (mmt) cc_final: 0.6041 (mmm) REVERT: A 767 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7083 (mp0) REVERT: A 821 GLU cc_start: 0.6689 (tt0) cc_final: 0.6301 (tt0) REVERT: A 890 TYR cc_start: 0.5873 (t80) cc_final: 0.5563 (t80) REVERT: A 956 LEU cc_start: 0.4148 (OUTLIER) cc_final: 0.3713 (tp) REVERT: A 959 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5382 (p0) outliers start: 23 outliers final: 11 residues processed: 124 average time/residue: 0.5228 time to fit residues: 70.2068 Evaluate side-chains 113 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 0.0670 chunk 9 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 331 ASN A 384 ASN ** A 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.235824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.184182 restraints weight = 8522.880| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.01 r_work: 0.4039 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10052 Z= 0.234 Angle : 0.764 17.433 13576 Z= 0.379 Chirality : 0.045 0.218 1490 Planarity : 0.005 0.046 1744 Dihedral : 4.615 20.737 1325 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 2.15 % Allowed : 23.67 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.29 (0.25), residues: 1197 helix: 1.34 (0.22), residues: 579 sheet: -0.93 (0.46), residues: 132 loop : -0.84 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 274 TYR 0.030 0.003 TYR A 988 PHE 0.018 0.003 PHE B 355 TRP 0.013 0.002 TRP A 552 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00566 (10052) covalent geometry : angle 0.76428 (13576) hydrogen bonds : bond 0.04665 ( 496) hydrogen bonds : angle 4.70066 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5134.20 seconds wall clock time: 87 minutes 53.67 seconds (5273.67 seconds total)