Starting phenix.real_space_refine on Thu Oct 22 21:31:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yae_72727/10_2026/9yae_72727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yae_72727/10_2026/9yae_72727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yae_72727/10_2026/9yae_72727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yae_72727/10_2026/9yae_72727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yae_72727/10_2026/9yae_72727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yae_72727/10_2026/9yae_72727.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 13 5.16 5 C 3704 2.51 5 N 981 2.21 5 O 1063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5764 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5733 Classifications: {'peptide': 752} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 17, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 4, 'GLU:plan': 25, 'ASP:plan': 19, 'ASN:plan1': 10, 'HIS:plan': 4, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 303 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.19 Number of scatterers: 5764 At special positions: 0 Unit cell: (75.68, 98.56, 117.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 3 15.00 O 1063 8.00 N 981 7.00 C 3704 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: 0.45 Conformation dependent library (CDL) restraints added in 267.7 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 45.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.555A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 15' Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.869A pdb=" N LYS A 20 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 removed outlier: 4.011A pdb=" N THR A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.745A pdb=" N LYS A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.814A pdb=" N ILE A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 4.061A pdb=" N LYS A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.927A pdb=" N TYR A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.519A pdb=" N LEU A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 327 through 337 removed outlier: 4.153A pdb=" N ASP A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.572A pdb=" N ILE A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.675A pdb=" N LEU A 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 426 through 440 removed outlier: 3.773A pdb=" N GLU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 removed outlier: 3.599A pdb=" N PHE A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 508 through 518 removed outlier: 4.010A pdb=" N ILE A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.634A pdb=" N SER A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 528 " --> pdb=" O HIS A 524 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.965A pdb=" N SER A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.541A pdb=" N SER A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.500A pdb=" N THR A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.031A pdb=" N ARG A 634 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.943A pdb=" N ALA A 644 " --> pdb=" O TRP A 640 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 664 removed outlier: 4.046A pdb=" N GLU A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.619A pdb=" N LEU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 694 removed outlier: 3.711A pdb=" N TYR A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 removed outlier: 4.549A pdb=" N SER A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 removed outlier: 3.568A pdb=" N ILE A 739 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.729A pdb=" N LYS A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.358A pdb=" N ILE A 25 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N PHE A 208 " --> pdb=" O ILE A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 143 removed outlier: 6.865A pdb=" N LYS A 141 " --> pdb=" O LEU A 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 425 removed outlier: 3.840A pdb=" N GLY A 347 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR A 346 " --> pdb=" O ILE A 448 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.583A pdb=" N ASN A 368 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL A 395 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER A 370 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS A 392 " --> pdb=" O LYS A 419 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 421 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 394 " --> pdb=" O VAL A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 545 through 546 165 hydrogen bonds defined for protein. 474 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: 0.89 Time building geometry restraints manager: 0.60 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: 1853 1.34 - 1.46: 1292 1.46 - 1.58: 2708 1.58 - 1.69: 8 1.69 - 1.81: 21 Bond restraints: 5882 Sorted by residual: bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.701 -0.257 1.10e-02 8.26e+03 5.46e+02 bond pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " ideal model delta sigma weight residual 1.526 1.301 0.225 1.10e-02 8.26e+03 4.19e+02 bond pdb=" C6 ATP A 801 " pdb=" N6 ATP A 801 " ideal model delta sigma weight residual 1.337 1.485 -0.148 1.10e-02 8.26e+03 1.81e+02 bond pdb=" C2' ATP A 801 " pdb=" O2' ATP A 801 " ideal model delta sigma weight residual 1.423 1.292 0.131 1.30e-02 5.92e+03 1.02e+02 bond pdb=" C1' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.416 1.309 0.107 1.30e-02 5.92e+03 6.79e+01 ... (remaining 5877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 7906 3.41 - 6.82: 63 6.82 - 10.23: 10 10.23 - 13.64: 1 13.64 - 17.06: 2 Bond angle restraints: 7982 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 122.81 17.06 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 123.16 13.67 1.00e+00 1.00e+00 1.87e+02 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.95 7.85 1.00e+00 1.00e+00 6.16e+01 angle pdb=" N1 ATP A 801 " pdb=" C2 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 128.69 121.35 7.34 1.00e+00 1.00e+00 5.38e+01 angle pdb=" N3 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N9 ATP A 801 " ideal model delta sigma weight residual 127.04 134.89 -7.85 1.15e+00 7.59e-01 4.68e+01 ... (remaining 7977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3246 17.91 - 35.83: 220 35.83 - 53.74: 42 53.74 - 71.66: 18 71.66 - 89.57: 2 Dihedral angle restraints: 3528 sinusoidal: 1297 harmonic: 2231 Sorted by residual: dihedral pdb=" CA THR A 64 " pdb=" C THR A 64 " pdb=" N GLN A 65 " pdb=" CA GLN A 65 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU A 224 " pdb=" C LEU A 224 " pdb=" N SER A 225 " pdb=" CA SER A 225 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER A 214 " pdb=" C SER A 214 " pdb=" N LEU A 215 " pdb=" CA LEU A 215 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 3525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 800 0.063 - 0.127: 111 0.127 - 0.190: 5 0.190 - 0.253: 2 0.253 - 0.317: 1 Chirality restraints: 919 Sorted by residual: chirality pdb=" CB ILE A 254 " pdb=" CA ILE A 254 " pdb=" CG1 ILE A 254 " pdb=" CG2 ILE A 254 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE A 382 " pdb=" CA ILE A 382 " pdb=" CG1 ILE A 382 " pdb=" CG2 ILE A 382 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 916 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 562 " -0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO A 563 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 25 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A 26 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 481 " 0.023 2.00e-02 2.50e+03 1.69e-02 4.98e+00 pdb=" CG PHE A 481 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 481 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 481 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 481 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 481 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 481 " 0.011 2.00e-02 2.50e+03 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 601 2.75 - 3.28: 6046 3.28 - 3.82: 8948 3.82 - 4.36: 10754 4.36 - 4.90: 17891 Nonbonded interactions: 44240 Sorted by model distance: nonbonded pdb=" O PHE A 230 " pdb=" N ILE A 254 " model vdw 2.208 3.120 nonbonded pdb=" O ASN A 718 " pdb=" OG SER A 721 " model vdw 2.268 3.040 nonbonded pdb=" N ARG A 151 " pdb=" O GLY A 595 " model vdw 2.292 3.120 nonbonded pdb=" OG SER A 600 " pdb=" OH TYR A 633 " model vdw 2.337 3.040 nonbonded pdb=" O ASN A 698 " pdb=" ND2 ASN A 698 " model vdw 2.338 3.120 ... (remaining 44235 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 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 : 0.007 0.257 5882 Z= 0.545 Angle : 0.827 17.055 7982 Z= 0.498 Chirality : 0.045 0.317 919 Planarity : 0.005 0.062 1011 Dihedral : 13.810 89.570 2076 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.56 (0.29), residues: 746 helix: -1.64 (0.28), residues: 316 sheet: -3.46 (0.46), residues: 99 loop : -2.63 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 284 TYR 0.015 0.001 TYR A 483 PHE 0.036 0.002 PHE A 481 TRP 0.018 0.003 TRP A 565 HIS 0.012 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.55 ( 5882) covalent geometry : angle 0.82678 / 0.50 ( 7982) hydrogen bonds : bond 0.21870 / 13.07 ( 165) hydrogen bonds : angle 7.76697 / 5.46 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7469 (mp) cc_final: 0.7129 (tp) REVERT: A 135 ASN cc_start: 0.7800 (t0) cc_final: 0.7443 (t0) REVERT: A 243 LEU cc_start: 0.6258 (mt) cc_final: 0.6049 (mt) REVERT: A 319 ARG cc_start: 0.7424 (tpt170) cc_final: 0.7157 (tpt90) REVERT: A 320 ASN cc_start: 0.8182 (t0) cc_final: 0.7527 (t0) REVERT: A 349 ARG cc_start: 0.7928 (mtp85) cc_final: 0.7706 (mtp-110) REVERT: A 373 SER cc_start: 0.8063 (t) cc_final: 0.7835 (p) REVERT: A 375 THR cc_start: 0.8336 (m) cc_final: 0.8024 (m) REVERT: A 557 VAL cc_start: 0.8526 (m) cc_final: 0.8218 (p) REVERT: A 568 ARG cc_start: 0.7748 (tpt90) cc_final: 0.7543 (tpt90) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0873 time to fit residues: 15.0773 Evaluate side-chains 113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 123 HIS ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN A 300 ASN A 392 HIS A 443 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.151492 restraints weight = 8880.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154732 restraints weight = 4854.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156870 restraints weight = 2947.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.158276 restraints weight = 1926.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.159227 restraints weight = 1335.990| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5882 Z= 0.168 Angle : 0.713 8.580 7982 Z= 0.364 Chirality : 0.045 0.231 919 Planarity : 0.005 0.051 1011 Dihedral : 8.607 72.755 840 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer: Outliers : 1.58 % Allowed : 9.11 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.29), residues: 746 helix: -1.28 (0.28), residues: 321 sheet: -3.57 (0.47), residues: 85 loop : -2.52 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 568 TYR 0.012 0.002 TYR A 140 PHE 0.029 0.002 PHE A 481 TRP 0.010 0.002 TRP A 269 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 5882) covalent geometry : angle 0.71338 / 0.36 ( 7982) hydrogen bonds : bond 0.03714 / 2.37 ( 165) hydrogen bonds : angle 5.50749 / 3.73 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7494 (mp) cc_final: 0.7217 (tp) REVERT: A 135 ASN cc_start: 0.7865 (t0) cc_final: 0.7511 (t0) REVERT: A 320 ASN cc_start: 0.8253 (t0) cc_final: 0.7594 (t0) REVERT: A 373 SER cc_start: 0.8161 (t) cc_final: 0.7895 (p) REVERT: A 375 THR cc_start: 0.8052 (m) cc_final: 0.7851 (m) REVERT: A 568 ARG cc_start: 0.7754 (tpt90) cc_final: 0.7460 (tpt90) REVERT: A 626 TYR cc_start: 0.5647 (m-80) cc_final: 0.5203 (m-80) outliers start: 9 outliers final: 6 residues processed: 125 average time/residue: 0.0902 time to fit residues: 14.4362 Evaluate side-chains 116 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 392 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [54, 67, 74, 36, 8, 42, 61, 43, 33, 29, 6] chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.0000 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 6 optimal weight: 0.4980 overall best weight: 0.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.161515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.149294 restraints weight = 8899.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.152655 restraints weight = 4832.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.154838 restraints weight = 2916.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.156318 restraints weight = 1907.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157330 restraints weight = 1324.016| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5882 Z= 0.145 Angle : 0.664 7.355 7982 Z= 0.341 Chirality : 0.043 0.206 919 Planarity : 0.004 0.045 1011 Dihedral : 8.394 73.136 840 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 2.45 % Allowed : 11.91 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.29), residues: 746 helix: -1.09 (0.28), residues: 316 sheet: -3.56 (0.48), residues: 91 loop : -2.48 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 348 TYR 0.011 0.001 TYR A 140 PHE 0.025 0.002 PHE A 481 TRP 0.008 0.002 TRP A 269 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5882) covalent geometry : angle 0.66418 / 0.34 ( 7982) hydrogen bonds : bond 0.03489 / 2.23 ( 165) hydrogen bonds : angle 5.21817 / 3.50 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7459 (mp) cc_final: 0.7154 (tp) REVERT: A 135 ASN cc_start: 0.7907 (t0) cc_final: 0.7533 (t0) REVERT: A 151 ARG cc_start: 0.8385 (mtp180) cc_final: 0.8156 (ttp-170) REVERT: A 258 ILE cc_start: 0.7717 (mm) cc_final: 0.7334 (mt) REVERT: A 320 ASN cc_start: 0.8212 (t0) cc_final: 0.7518 (t0) REVERT: A 373 SER cc_start: 0.8142 (t) cc_final: 0.7848 (p) REVERT: A 375 THR cc_start: 0.8048 (m) cc_final: 0.7841 (m) REVERT: A 568 ARG cc_start: 0.7741 (tpt90) cc_final: 0.7495 (tpt90) REVERT: A 626 TYR cc_start: 0.5898 (m-80) cc_final: 0.4958 (m-80) REVERT: A 649 ILE cc_start: 0.7904 (mm) cc_final: 0.7599 (pt) outliers start: 14 outliers final: 7 residues processed: 122 average time/residue: 0.0777 time to fit residues: 12.3882 Evaluate side-chains 115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [18, 5, 43, 39, 25, 31, 36, 56, 0, 66, 32] chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 56 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.160726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148534 restraints weight = 8840.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151895 restraints weight = 4805.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153949 restraints weight = 2898.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155473 restraints weight = 1920.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156465 restraints weight = 1326.624| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5882 Z= 0.142 Angle : 0.645 6.697 7982 Z= 0.333 Chirality : 0.043 0.174 919 Planarity : 0.004 0.042 1011 Dihedral : 8.232 73.612 840 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Rotamer: Outliers : 2.28 % Allowed : 14.36 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.29), residues: 746 helix: -0.93 (0.28), residues: 315 sheet: -3.45 (0.49), residues: 91 loop : -2.53 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.018 0.001 TYR A 252 PHE 0.023 0.002 PHE A 481 TRP 0.007 0.001 TRP A 269 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5882) covalent geometry : angle 0.64525 / 0.33 ( 7982) hydrogen bonds : bond 0.03234 / 2.08 ( 165) hydrogen bonds : angle 5.07868 / 3.40 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7462 (mp) cc_final: 0.7136 (tp) REVERT: A 135 ASN cc_start: 0.7911 (t0) cc_final: 0.7543 (t0) REVERT: A 258 ILE cc_start: 0.7681 (mm) cc_final: 0.7312 (mt) REVERT: A 290 ASP cc_start: 0.7243 (m-30) cc_final: 0.6288 (m-30) REVERT: A 320 ASN cc_start: 0.8233 (t0) cc_final: 0.7510 (t0) REVERT: A 568 ARG cc_start: 0.7732 (tpt90) cc_final: 0.7455 (tpt90) REVERT: A 596 PHE cc_start: 0.7311 (m-10) cc_final: 0.7105 (m-10) REVERT: A 626 TYR cc_start: 0.5840 (m-80) cc_final: 0.4531 (m-80) REVERT: A 649 ILE cc_start: 0.7877 (mm) cc_final: 0.7538 (pt) outliers start: 13 outliers final: 12 residues processed: 120 average time/residue: 0.0814 time to fit residues: 12.7417 Evaluate side-chains 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [36, 15, 41, 73, 45, 11, 25, 64, 31, 32, 35] chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 41 optimal weight: 0.0370 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 11 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.0914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 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 = 0.4144 r_free = 0.4144 target = 0.164389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.152039 restraints weight = 9125.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155516 restraints weight = 4904.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.157781 restraints weight = 2921.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.159223 restraints weight = 1886.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.160225 restraints weight = 1304.144| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5882 Z= 0.106 Angle : 0.617 8.867 7982 Z= 0.317 Chirality : 0.042 0.264 919 Planarity : 0.003 0.039 1011 Dihedral : 7.898 73.573 840 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 2.28 % Allowed : 16.11 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.30), residues: 746 helix: -0.80 (0.28), residues: 324 sheet: -3.46 (0.51), residues: 76 loop : -2.58 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.017 0.001 TYR A 252 PHE 0.020 0.001 PHE A 481 TRP 0.007 0.001 TRP A 121 HIS 0.006 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 5882) covalent geometry : angle 0.61688 / 0.32 ( 7982) hydrogen bonds : bond 0.02845 / 1.85 ( 165) hydrogen bonds : angle 4.76901 / 3.15 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7431 (mp) cc_final: 0.7116 (tp) REVERT: A 135 ASN cc_start: 0.7801 (t0) cc_final: 0.7499 (t0) REVERT: A 258 ILE cc_start: 0.7573 (mm) cc_final: 0.7227 (mt) REVERT: A 290 ASP cc_start: 0.7110 (m-30) cc_final: 0.6176 (m-30) REVERT: A 320 ASN cc_start: 0.8081 (t0) cc_final: 0.7268 (t0) REVERT: A 373 SER cc_start: 0.8138 (t) cc_final: 0.7831 (p) REVERT: A 568 ARG cc_start: 0.7661 (tpt90) cc_final: 0.7434 (tpt90) REVERT: A 596 PHE cc_start: 0.7242 (m-10) cc_final: 0.6892 (m-10) REVERT: A 626 TYR cc_start: 0.5907 (m-80) cc_final: 0.4480 (m-80) outliers start: 13 outliers final: 11 residues processed: 124 average time/residue: 0.0811 time to fit residues: 13.0036 Evaluate side-chains 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [30, 0, 20, 53, 26, 44, 23, 59, 74, 56, 7] chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 111 HIS A 128 ASN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.160787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148806 restraints weight = 8945.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152047 restraints weight = 4866.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.154185 restraints weight = 2958.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155617 restraints weight = 1938.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156579 restraints weight = 1347.508| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5882 Z= 0.160 Angle : 0.653 7.606 7982 Z= 0.338 Chirality : 0.043 0.180 919 Planarity : 0.004 0.039 1011 Dihedral : 8.033 74.196 840 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer: Outliers : 3.15 % Allowed : 16.64 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.30), residues: 746 helix: -0.79 (0.29), residues: 316 sheet: -3.40 (0.49), residues: 92 loop : -2.49 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.019 0.002 TYR A 252 PHE 0.019 0.002 PHE A 481 TRP 0.008 0.002 TRP A 269 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 5882) covalent geometry : angle 0.65299 / 0.34 ( 7982) hydrogen bonds : bond 0.03167 / 2.05 ( 165) hydrogen bonds : angle 4.94492 / 3.31 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: A 72 LEU cc_start: 0.7515 (mp) cc_final: 0.7196 (tp) REVERT: A 135 ASN cc_start: 0.7884 (t0) cc_final: 0.7513 (t0) REVERT: A 258 ILE cc_start: 0.7596 (mm) cc_final: 0.7224 (mt) REVERT: A 290 ASP cc_start: 0.7156 (m-30) cc_final: 0.6270 (m-30) REVERT: A 320 ASN cc_start: 0.8155 (t0) cc_final: 0.7499 (t0) REVERT: A 373 SER cc_start: 0.8220 (t) cc_final: 0.7886 (p) REVERT: A 568 ARG cc_start: 0.7702 (tpt90) cc_final: 0.7457 (tpt170) REVERT: A 596 PHE cc_start: 0.7400 (m-10) cc_final: 0.7038 (m-80) REVERT: A 626 TYR cc_start: 0.5991 (m-80) cc_final: 0.4427 (m-80) REVERT: A 688 GLN cc_start: 0.7867 (mt0) cc_final: 0.7663 (mt0) REVERT: A 740 GLN cc_start: 0.6879 (tm-30) cc_final: 0.6610 (tm-30) outliers start: 18 outliers final: 11 residues processed: 129 average time/residue: 0.0804 time to fit residues: 13.5498 Evaluate side-chains 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [40, 31, 58, 13, 14, 30, 47, 23, 35, 49, 3] chunk 40 optimal weight: 0.0010 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.0000 chunk 30 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 111 HIS ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 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 = 0.4123 r_free = 0.4123 target = 0.162756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150690 restraints weight = 8952.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153987 restraints weight = 4889.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156155 restraints weight = 2968.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157534 restraints weight = 1943.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.158510 restraints weight = 1361.910| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5882 Z= 0.124 Angle : 0.631 7.500 7982 Z= 0.325 Chirality : 0.042 0.195 919 Planarity : 0.004 0.037 1011 Dihedral : 7.891 75.461 840 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 2.63 % Allowed : 17.69 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.30), residues: 746 helix: -0.76 (0.29), residues: 321 sheet: -3.18 (0.53), residues: 83 loop : -2.47 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.016 0.001 TYR A 252 PHE 0.025 0.002 PHE A 706 TRP 0.007 0.001 TRP A 269 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 5882) covalent geometry : angle 0.63146 / 0.33 ( 7982) hydrogen bonds : bond 0.02891 / 1.88 ( 165) hydrogen bonds : angle 4.81200 / 3.20 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: A 72 LEU cc_start: 0.7479 (mp) cc_final: 0.7153 (tp) REVERT: A 135 ASN cc_start: 0.7877 (t0) cc_final: 0.7550 (t0) REVERT: A 258 ILE cc_start: 0.7503 (mm) cc_final: 0.7126 (mt) REVERT: A 290 ASP cc_start: 0.7185 (m-30) cc_final: 0.6964 (m-30) REVERT: A 320 ASN cc_start: 0.8105 (t0) cc_final: 0.7408 (t0) REVERT: A 373 SER cc_start: 0.8184 (t) cc_final: 0.7856 (p) REVERT: A 568 ARG cc_start: 0.7671 (tpt90) cc_final: 0.7462 (tpt170) REVERT: A 596 PHE cc_start: 0.7380 (m-10) cc_final: 0.6997 (m-10) REVERT: A 626 TYR cc_start: 0.6026 (m-80) cc_final: 0.4379 (m-80) REVERT: A 740 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6555 (tm-30) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.0794 time to fit residues: 13.2563 Evaluate side-chains 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [19, 56, 39, 9, 22, 40, 42, 51, 32, 60, 5] chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149858 restraints weight = 8901.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.153097 restraints weight = 4865.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.155212 restraints weight = 2954.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156528 restraints weight = 1946.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157578 restraints weight = 1383.837| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5882 Z= 0.137 Angle : 0.642 8.177 7982 Z= 0.330 Chirality : 0.043 0.247 919 Planarity : 0.004 0.037 1011 Dihedral : 7.921 74.620 840 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 2.80 % Allowed : 19.61 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.30), residues: 746 helix: -0.80 (0.29), residues: 322 sheet: -3.12 (0.53), residues: 83 loop : -2.42 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 348 TYR 0.010 0.001 TYR A 252 PHE 0.019 0.002 PHE A 466 TRP 0.007 0.001 TRP A 269 HIS 0.005 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5882) covalent geometry : angle 0.64199 / 0.33 ( 7982) hydrogen bonds : bond 0.02988 / 1.95 ( 165) hydrogen bonds : angle 4.84094 / 3.23 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: A 72 LEU cc_start: 0.7511 (mp) cc_final: 0.7181 (tp) REVERT: A 135 ASN cc_start: 0.7930 (t0) cc_final: 0.7563 (t0) REVERT: A 231 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7334 (tptp) REVERT: A 258 ILE cc_start: 0.7463 (mm) cc_final: 0.7091 (mt) REVERT: A 290 ASP cc_start: 0.7153 (m-30) cc_final: 0.6944 (m-30) REVERT: A 320 ASN cc_start: 0.8077 (t0) cc_final: 0.7422 (t0) REVERT: A 373 SER cc_start: 0.8218 (t) cc_final: 0.7842 (p) REVERT: A 568 ARG cc_start: 0.7677 (tpt90) cc_final: 0.7441 (tpt170) REVERT: A 596 PHE cc_start: 0.7410 (m-10) cc_final: 0.7001 (m-80) REVERT: A 625 ILE cc_start: 0.8179 (pt) cc_final: 0.7888 (mp) REVERT: A 740 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6525 (tm130) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.0846 time to fit residues: 13.2780 Evaluate side-chains 124 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 740 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [16, 48, 49, 67, 50, 65, 71, 32, 4, 3, 8] chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.157726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.145942 restraints weight = 8969.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149069 restraints weight = 4955.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.151147 restraints weight = 3028.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152516 restraints weight = 2000.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.153485 restraints weight = 1404.124| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5882 Z= 0.238 Angle : 0.741 10.160 7982 Z= 0.383 Chirality : 0.047 0.264 919 Planarity : 0.004 0.042 1011 Dihedral : 8.334 75.255 840 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.28 % Favored : 84.72 % Rotamer: Outliers : 2.45 % Allowed : 19.61 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.29), residues: 746 helix: -1.02 (0.28), residues: 322 sheet: -3.29 (0.55), residues: 79 loop : -2.53 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 348 TYR 0.017 0.002 TYR A 252 PHE 0.022 0.002 PHE A 286 TRP 0.012 0.002 TRP A 269 HIS 0.008 0.002 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 ( 5882) covalent geometry : angle 0.74117 / 0.38 ( 7982) hydrogen bonds : bond 0.03577 / 2.35 ( 165) hydrogen bonds : angle 5.32173 / 3.61 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: A 72 LEU cc_start: 0.7568 (mp) cc_final: 0.7255 (tp) REVERT: A 135 ASN cc_start: 0.7964 (t0) cc_final: 0.7557 (t0) REVERT: A 231 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7418 (tptp) REVERT: A 258 ILE cc_start: 0.7554 (mm) cc_final: 0.7178 (mt) REVERT: A 286 PHE cc_start: 0.7691 (p90) cc_final: 0.7392 (p90) REVERT: A 290 ASP cc_start: 0.7138 (m-30) cc_final: 0.6274 (m-30) REVERT: A 320 ASN cc_start: 0.8125 (t0) cc_final: 0.7519 (t0) REVERT: A 559 ILE cc_start: 0.7917 (mm) cc_final: 0.7710 (mm) REVERT: A 568 ARG cc_start: 0.7732 (tpt90) cc_final: 0.7406 (tpt170) REVERT: A 596 PHE cc_start: 0.7568 (m-10) cc_final: 0.7187 (m-80) REVERT: A 740 GLN cc_start: 0.6950 (tm130) cc_final: 0.6556 (tm130) outliers start: 14 outliers final: 11 residues processed: 121 average time/residue: 0.0716 time to fit residues: 11.5537 Evaluate side-chains 118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 667 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [21, 62, 3, 60, 24, 64, 25, 23, 33, 67, 45] chunk 21 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 0.0170 chunk 25 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149137 restraints weight = 8953.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.152382 restraints weight = 4879.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154497 restraints weight = 2963.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.155938 restraints weight = 1951.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.156810 restraints weight = 1358.901| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5882 Z= 0.135 Angle : 0.658 7.873 7982 Z= 0.341 Chirality : 0.043 0.235 919 Planarity : 0.004 0.039 1011 Dihedral : 8.050 76.616 840 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 2.10 % Allowed : 20.32 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.30), residues: 746 helix: -0.80 (0.29), residues: 316 sheet: -2.91 (0.59), residues: 75 loop : -2.48 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.013 0.001 TYR A 432 PHE 0.021 0.002 PHE A 286 TRP 0.006 0.001 TRP A 269 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5882) covalent geometry : angle 0.65815 / 0.34 ( 7982) hydrogen bonds : bond 0.03012 / 1.97 ( 165) hydrogen bonds : angle 5.00594 / 3.35 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: A 72 LEU cc_start: 0.7516 (mp) cc_final: 0.7221 (tp) REVERT: A 135 ASN cc_start: 0.7846 (t0) cc_final: 0.7482 (t0) REVERT: A 257 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.6994 (m) REVERT: A 258 ILE cc_start: 0.7398 (mm) cc_final: 0.7058 (mt) REVERT: A 286 PHE cc_start: 0.7678 (p90) cc_final: 0.7214 (p90) REVERT: A 290 ASP cc_start: 0.7153 (m-30) cc_final: 0.6261 (m-30) REVERT: A 320 ASN cc_start: 0.8055 (t0) cc_final: 0.7406 (t0) REVERT: A 373 SER cc_start: 0.8242 (t) cc_final: 0.7883 (p) REVERT: A 508 MET cc_start: 0.6669 (tpp) cc_final: 0.6388 (ttm) REVERT: A 596 PHE cc_start: 0.7596 (m-10) cc_final: 0.7245 (m-80) REVERT: A 625 ILE cc_start: 0.8179 (pt) cc_final: 0.7900 (mp) outliers start: 12 outliers final: 8 residues processed: 117 average time/residue: 0.0811 time to fit residues: 12.3598 Evaluate side-chains 115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [56, 38, 18, 37, 44, 6, 54, 47, 21, 67, 32] chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.157855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145449 restraints weight = 8886.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148724 restraints weight = 4890.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150904 restraints weight = 2991.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152350 restraints weight = 1970.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.153334 restraints weight = 1383.737| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5882 Z= 0.185 Angle : 0.698 9.112 7982 Z= 0.362 Chirality : 0.045 0.274 919 Planarity : 0.004 0.041 1011 Dihedral : 8.219 76.043 840 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 1.75 % Allowed : 21.02 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.29), residues: 746 helix: -0.98 (0.28), residues: 322 sheet: -3.16 (0.57), residues: 79 loop : -2.72 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 348 TYR 0.013 0.002 TYR A 252 PHE 0.021 0.002 PHE A 286 TRP 0.010 0.002 TRP A 269 HIS 0.007 0.002 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 5882) covalent geometry : angle 0.69781 / 0.36 ( 7982) hydrogen bonds : bond 0.03287 / 2.15 ( 165) hydrogen bonds : angle 5.16650 / 3.47 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1152.30 seconds wall clock time: 20 minutes 34.14 seconds (1234.14 seconds total)