Starting phenix.real_space_refine on Thu Jul 2 08:58:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxb_29530/07_2026/8fxb_29530.cif" } resolution = 3.1 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= 0.107 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 42 5.16 5 C 5041 2.51 5 N 1318 2.21 5 O 1511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7912 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 769 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 4789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4789 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561} Chain breaks: 1 Chain: "E" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1296 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain breaks: 2 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.81, per 1000 atoms: 0.23 Number of scatterers: 7912 At special positions: 0 Unit cell: (85, 100, 130, 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 42 16.00 O 1511 8.00 N 1318 7.00 C 5041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.08 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.01 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.01 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 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 Links applied BETA1-6 " NAG B 1 " - " FUC B 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 90 " " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 546 " " NAG A 704 " - " ASN A 322 " " NAG A 705 " - " ASN A 103 " " NAG B 1 " - " ASN E 343 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 433.4 milliseconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 44.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.044A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.594A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.068A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.557A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.581A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.537A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.784A pdb=" N SER A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.846A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 221 through 249 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.783A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 402 through 413 removed outlier: 5.135A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.621A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.769A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 515 through 533 removed outlier: 4.197A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.736A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.558A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.724A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.724A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA8, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.735A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'E' and resid 451 through 453 removed outlier: 4.774A pdb=" N TYR E 451 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 473 through 474 368 hydrogen bonds defined for protein. 975 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: 1.44 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1626 1.33 - 1.45: 2152 1.45 - 1.58: 4277 1.58 - 1.71: 1 1.71 - 1.83: 66 Bond restraints: 8122 Sorted by residual: bond pdb=" N ASP A 494 " pdb=" CA ASP A 494 " ideal model delta sigma weight residual 1.457 1.489 -0.033 6.40e-03 2.44e+04 2.64e+01 bond pdb=" N GLN E 493 " pdb=" CA GLN E 493 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.31e-02 5.83e+03 9.39e+00 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.589 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" N PHE E 456 " pdb=" CA PHE E 456 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.27e-02 6.20e+03 7.98e+00 ... (remaining 8117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 10553 2.52 - 5.04: 390 5.04 - 7.56: 79 7.56 - 10.08: 4 10.08 - 12.60: 1 Bond angle restraints: 11027 Sorted by residual: angle pdb=" C TYR E 449 " pdb=" CA TYR E 449 " pdb=" CB TYR E 449 " ideal model delta sigma weight residual 111.88 99.28 12.60 1.41e+00 5.03e-01 7.99e+01 angle pdb=" C GLY A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta sigma weight residual 119.76 127.52 -7.76 1.03e+00 9.43e-01 5.68e+01 angle pdb=" C SER A 257 " pdb=" N PRO A 258 " pdb=" CA PRO A 258 " ideal model delta sigma weight residual 119.56 127.21 -7.65 1.02e+00 9.61e-01 5.62e+01 angle pdb=" C ARG E 498 " pdb=" N PRO E 499 " pdb=" CA PRO E 499 " ideal model delta sigma weight residual 119.56 126.96 -7.40 1.01e+00 9.80e-01 5.37e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.89 127.20 -7.31 1.02e+00 9.61e-01 5.14e+01 ... (remaining 11022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.97: 4366 12.97 - 25.94: 234 25.94 - 38.91: 67 38.91 - 51.88: 28 51.88 - 64.85: 23 Dihedral angle restraints: 4718 sinusoidal: 1885 harmonic: 2833 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 60.95 32.05 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 61.16 31.84 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" C TYR E 449 " pdb=" N TYR E 449 " pdb=" CA TYR E 449 " pdb=" CB TYR E 449 " ideal model delta harmonic sigma weight residual -122.60 -113.36 -9.24 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 828 0.067 - 0.134: 266 0.134 - 0.200: 73 0.200 - 0.267: 11 0.267 - 0.334: 6 Chirality restraints: 1184 Sorted by residual: chirality pdb=" C1 FUC B 2 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 2 " pdb=" O5 FUC B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.07e+01 chirality pdb=" C2 NAG A 703 " pdb=" C1 NAG A 703 " pdb=" C3 NAG A 703 " pdb=" N2 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C1 NAG A 705 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 705 " pdb=" O5 NAG A 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1181 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " -0.096 2.00e-02 2.50e+03 7.89e-02 7.78e+01 pdb=" C7 NAG A 704 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " 0.125 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 705 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG A 705 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 705 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 705 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A 705 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 320 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C LEU A 320 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 320 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 321 " 0.016 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 25 2.60 - 3.17: 6708 3.17 - 3.75: 11708 3.75 - 4.32: 17687 4.32 - 4.90: 28333 Nonbonded interactions: 64461 Sorted by model distance: nonbonded pdb=" O ASP A 471 " pdb=" OE2 GLU A 495 " model vdw 2.024 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.271 3.120 nonbonded pdb=" CB LYS L 40 " pdb=" OE1 GLN L 43 " model vdw 2.308 3.440 nonbonded pdb=" O GLU A 495 " pdb=" N TYR A 497 " model vdw 2.340 3.120 nonbonded pdb=" O TYR E 449 " pdb=" CB TYR E 449 " model vdw 2.440 2.752 ... (remaining 64456 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: 1.160 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.930 Find NCS groups from input model: 0.030 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.011 0.062 8137 Z= 0.641 Angle : 1.241 15.581 11064 Z= 0.847 Chirality : 0.073 0.334 1184 Planarity : 0.005 0.079 1410 Dihedral : 10.645 64.853 2882 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.22 % Favored : 96.36 % Rotamer: Outliers : 0.59 % Allowed : 2.02 % Favored : 97.39 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.65 % 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: -0.59 (0.26), residues: 962 helix: -0.84 (0.24), residues: 382 sheet: 0.63 (0.39), residues: 146 loop : -0.13 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.031 0.004 TYR E 495 PHE 0.021 0.003 PHE L 98 TRP 0.018 0.003 TRP H 117 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01119 / 0.64 ( 8122) covalent geometry : angle 1.20953 / 0.84 (11027) SS BOND : bond 0.02926 / 1.52 ( 8) SS BOND : angle 4.41897 / 2.56 ( 16) hydrogen bonds : bond 0.20275 / 13.81 ( 353) hydrogen bonds : angle 7.09615 / 4.84 ( 975) link_BETA1-6 : bond 0.04865 / 2.56 ( 1) link_BETA1-6 : angle 2.96652 / 1.51 ( 3) link_NAG-ASN : bond 0.04037 / 2.27 ( 6) link_NAG-ASN : angle 5.65421 / 2.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.297 Fit side-chains REVERT: A 401 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8592 (t-90) outliers start: 5 outliers final: 3 residues processed: 175 average time/residue: 0.0764 time to fit residues: 19.2529 Evaluate side-chains 97 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 55 ASN A 33 ASN A 96 GLN A 535 HIS A 586 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.186694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162484 restraints weight = 9764.833| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.05 r_work: 0.3840 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8137 Z= 0.132 Angle : 0.566 7.565 11064 Z= 0.300 Chirality : 0.042 0.165 1184 Planarity : 0.004 0.066 1410 Dihedral : 5.087 56.542 1069 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.95 % Allowed : 7.83 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.46 (0.27), residues: 962 helix: 0.51 (0.27), residues: 384 sheet: 0.69 (0.40), residues: 150 loop : 0.15 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 177 TYR 0.016 0.001 TYR E 495 PHE 0.011 0.001 PHE E 456 TRP 0.012 0.001 TRP A 275 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8122) covalent geometry : angle 0.56025 / 0.30 (11027) SS BOND : bond 0.00449 / 0.26 ( 8) SS BOND : angle 1.15091 / 0.68 ( 16) hydrogen bonds : bond 0.05264 / 3.57 ( 353) hydrogen bonds : angle 4.98185 / 3.40 ( 975) link_BETA1-6 : bond 0.00466 / 0.25 ( 1) link_BETA1-6 : angle 1.56838 / 0.77 ( 3) link_NAG-ASN : bond 0.00466 / 0.23 ( 6) link_NAG-ASN : angle 1.65528 / 0.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7370 (mm110) cc_final: 0.6950 (tt0) REVERT: A 95 LEU cc_start: 0.6281 (pp) cc_final: 0.4903 (tp) REVERT: A 111 ASP cc_start: 0.7277 (t0) cc_final: 0.6828 (m-30) REVERT: A 401 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8667 (t70) REVERT: A 455 MET cc_start: 0.7600 (tmm) cc_final: 0.7271 (ttp) outliers start: 8 outliers final: 3 residues processed: 124 average time/residue: 0.0876 time to fit residues: 15.2426 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.0370 chunk 40 optimal weight: 0.0670 chunk 20 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 96 GLN A 101 GLN A 228 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.183952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.159084 restraints weight = 9702.927| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.05 r_work: 0.3800 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8137 Z= 0.127 Angle : 0.522 6.064 11064 Z= 0.272 Chirality : 0.041 0.146 1184 Planarity : 0.004 0.059 1410 Dihedral : 4.341 55.816 1064 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.19 % Allowed : 8.07 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.58 (0.27), residues: 962 helix: 0.71 (0.27), residues: 379 sheet: 0.71 (0.42), residues: 139 loop : 0.14 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.025 0.001 TYR E 365 PHE 0.012 0.001 PHE E 456 TRP 0.012 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8122) covalent geometry : angle 0.51794 / 0.27 (11027) SS BOND : bond 0.00374 / 0.22 ( 8) SS BOND : angle 0.96735 / 0.58 ( 16) hydrogen bonds : bond 0.04477 / 3.04 ( 353) hydrogen bonds : angle 4.62716 / 3.17 ( 975) link_BETA1-6 : bond 0.00338 / 0.18 ( 1) link_BETA1-6 : angle 1.30235 / 0.68 ( 3) link_NAG-ASN : bond 0.00177 / 0.08 ( 6) link_NAG-ASN : angle 1.48423 / 0.86 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.296 Fit side-chains REVERT: L 24 ARG cc_start: 0.6444 (mmm-85) cc_final: 0.6160 (tpp80) REVERT: H 62 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: A 95 LEU cc_start: 0.6266 (pp) cc_final: 0.4893 (tp) REVERT: A 360 MET cc_start: 0.7483 (ttt) cc_final: 0.7267 (ttp) REVERT: A 423 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7901 (mp) REVERT: A 455 MET cc_start: 0.7566 (tmm) cc_final: 0.7272 (ttp) outliers start: 10 outliers final: 3 residues processed: 117 average time/residue: 0.0861 time to fit residues: 14.1752 Evaluate side-chains 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN H 65 GLN A 33 ASN A 96 GLN A 228 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN E 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149926 restraints weight = 10156.319| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.10 r_work: 0.3698 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 8137 Z= 0.264 Angle : 0.717 8.703 11064 Z= 0.366 Chirality : 0.048 0.217 1184 Planarity : 0.006 0.063 1410 Dihedral : 4.889 58.505 1062 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.54 % Allowed : 9.85 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.01 (0.26), residues: 962 helix: 0.09 (0.26), residues: 374 sheet: 0.41 (0.40), residues: 147 loop : -0.07 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 460 TYR 0.026 0.003 TYR A 41 PHE 0.026 0.003 PHE A 438 TRP 0.018 0.002 TRP H 117 HIS 0.006 0.002 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 ( 8122) covalent geometry : angle 0.71051 / 0.36 (11027) SS BOND : bond 0.00787 / 0.49 ( 8) SS BOND : angle 1.74718 / 1.06 ( 16) hydrogen bonds : bond 0.05828 / 3.90 ( 353) hydrogen bonds : angle 4.88542 / 3.34 ( 975) link_BETA1-6 : bond 0.00067 / 0.04 ( 1) link_BETA1-6 : angle 2.01168 / 1.08 ( 3) link_NAG-ASN : bond 0.00408 / 0.23 ( 6) link_NAG-ASN : angle 1.91173 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6725 (mmm-85) cc_final: 0.6401 (tpp80) REVERT: H 43 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7292 (tt0) REVERT: H 82 GLU cc_start: 0.7937 (tt0) cc_final: 0.7725 (tt0) REVERT: A 106 SER cc_start: 0.5988 (m) cc_final: 0.5750 (p) REVERT: A 423 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 455 MET cc_start: 0.7872 (tmm) cc_final: 0.7446 (ttp) REVERT: A 497 TYR cc_start: 0.6991 (m-80) cc_final: 0.6735 (m-80) outliers start: 13 outliers final: 7 residues processed: 117 average time/residue: 0.0869 time to fit residues: 14.3595 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 96 GLN A 210 ASN A 228 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.176686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151610 restraints weight = 9994.607| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.04 r_work: 0.3721 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8137 Z= 0.175 Angle : 0.604 9.229 11064 Z= 0.305 Chirality : 0.043 0.206 1184 Planarity : 0.005 0.055 1410 Dihedral : 4.645 59.432 1062 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.54 % Allowed : 10.32 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.16 (0.27), residues: 962 helix: 0.39 (0.27), residues: 367 sheet: 0.45 (0.41), residues: 147 loop : -0.10 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 460 TYR 0.018 0.002 TYR E 495 PHE 0.015 0.002 PHE A 438 TRP 0.016 0.002 TRP A 477 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 8122) covalent geometry : angle 0.59849 / 0.30 (11027) SS BOND : bond 0.00427 / 0.25 ( 8) SS BOND : angle 1.10725 / 0.65 ( 16) hydrogen bonds : bond 0.04779 / 3.20 ( 353) hydrogen bonds : angle 4.63205 / 3.16 ( 975) link_BETA1-6 : bond 0.00341 / 0.18 ( 1) link_BETA1-6 : angle 1.57278 / 0.86 ( 3) link_NAG-ASN : bond 0.00262 / 0.12 ( 6) link_NAG-ASN : angle 1.79547 / 1.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6515 (mmm-85) cc_final: 0.6271 (tpp80) REVERT: H 43 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7284 (tt0) REVERT: A 423 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 455 MET cc_start: 0.7714 (tmm) cc_final: 0.7353 (ttp) REVERT: A 497 TYR cc_start: 0.6878 (m-80) cc_final: 0.6645 (m-80) REVERT: A 610 TRP cc_start: 0.6571 (t60) cc_final: 0.6300 (t60) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 0.0819 time to fit residues: 12.8644 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN A 228 HIS ** A 522 GLN ** 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 = 0.4111 r_free = 0.4111 target = 0.175936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150273 restraints weight = 10177.816| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.11 r_work: 0.3711 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8137 Z= 0.194 Angle : 0.625 9.176 11064 Z= 0.315 Chirality : 0.044 0.228 1184 Planarity : 0.005 0.056 1410 Dihedral : 4.697 59.511 1062 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.54 % Allowed : 10.68 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.03 (0.27), residues: 962 helix: 0.27 (0.26), residues: 373 sheet: 0.38 (0.41), residues: 147 loop : -0.17 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 460 TYR 0.020 0.002 TYR E 495 PHE 0.018 0.002 PHE A 438 TRP 0.017 0.002 TRP A 477 HIS 0.004 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 8122) covalent geometry : angle 0.61952 / 0.31 (11027) SS BOND : bond 0.00391 / 0.21 ( 8) SS BOND : angle 1.03284 / 0.62 ( 16) hydrogen bonds : bond 0.04928 / 3.29 ( 353) hydrogen bonds : angle 4.61914 / 3.16 ( 975) link_BETA1-6 : bond 0.00257 / 0.14 ( 1) link_BETA1-6 : angle 1.71637 / 0.94 ( 3) link_NAG-ASN : bond 0.00308 / 0.16 ( 6) link_NAG-ASN : angle 1.86453 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6499 (mmm-85) cc_final: 0.6235 (tpp80) REVERT: H 43 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7296 (tt0) REVERT: H 82 GLU cc_start: 0.7905 (tt0) cc_final: 0.7616 (tt0) REVERT: A 255 TYR cc_start: 0.7510 (m-80) cc_final: 0.7297 (m-10) REVERT: A 423 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 455 MET cc_start: 0.7702 (tmm) cc_final: 0.7297 (ttp) REVERT: A 497 TYR cc_start: 0.6938 (m-80) cc_final: 0.6683 (m-80) REVERT: A 610 TRP cc_start: 0.6796 (t60) cc_final: 0.6554 (t60) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.0834 time to fit residues: 13.0791 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 472 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN A 228 HIS ** A 522 GLN ** 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 = 0.4119 r_free = 0.4119 target = 0.176507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151086 restraints weight = 10092.849| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.10 r_work: 0.3719 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8137 Z= 0.168 Angle : 0.597 8.728 11064 Z= 0.300 Chirality : 0.043 0.221 1184 Planarity : 0.005 0.054 1410 Dihedral : 4.601 58.753 1062 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.54 % Allowed : 11.15 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.10 (0.27), residues: 962 helix: 0.38 (0.26), residues: 380 sheet: 0.43 (0.42), residues: 146 loop : -0.20 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.017 0.002 TYR E 495 PHE 0.014 0.002 PHE A 438 TRP 0.017 0.002 TRP A 477 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 8122) covalent geometry : angle 0.59114 / 0.30 (11027) SS BOND : bond 0.00351 / 0.19 ( 8) SS BOND : angle 0.89736 / 0.54 ( 16) hydrogen bonds : bond 0.04619 / 3.09 ( 353) hydrogen bonds : angle 4.53431 / 3.09 ( 975) link_BETA1-6 : bond 0.00161 / 0.08 ( 1) link_BETA1-6 : angle 1.62872 / 0.88 ( 3) link_NAG-ASN : bond 0.00262 / 0.12 ( 6) link_NAG-ASN : angle 1.88150 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6439 (mmm-85) cc_final: 0.6164 (tpp80) REVERT: A 423 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 455 MET cc_start: 0.7710 (tmm) cc_final: 0.7317 (ttp) REVERT: A 497 TYR cc_start: 0.6900 (m-80) cc_final: 0.6644 (m-80) REVERT: A 610 TRP cc_start: 0.6818 (t60) cc_final: 0.6594 (t60) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.0816 time to fit residues: 12.5694 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 472 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 86 optimal weight: 0.0040 chunk 79 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.177291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152268 restraints weight = 10036.606| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.04 r_work: 0.3732 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8137 Z= 0.140 Angle : 0.564 8.550 11064 Z= 0.283 Chirality : 0.042 0.207 1184 Planarity : 0.004 0.053 1410 Dihedral : 4.475 58.819 1062 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.42 % Allowed : 11.63 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.25 (0.27), residues: 962 helix: 0.58 (0.26), residues: 381 sheet: 0.40 (0.42), residues: 148 loop : -0.15 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.017 0.002 TYR A 50 PHE 0.012 0.001 PHE A 438 TRP 0.016 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8122) covalent geometry : angle 0.55871 / 0.28 (11027) SS BOND : bond 0.00297 / 0.16 ( 8) SS BOND : angle 0.81612 / 0.49 ( 16) hydrogen bonds : bond 0.04273 / 2.87 ( 353) hydrogen bonds : angle 4.42513 / 3.02 ( 975) link_BETA1-6 : bond 0.00100 / 0.05 ( 1) link_BETA1-6 : angle 1.56257 / 0.84 ( 3) link_NAG-ASN : bond 0.00246 / 0.11 ( 6) link_NAG-ASN : angle 1.79115 / 1.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6407 (mmm-85) cc_final: 0.6166 (tpp80) REVERT: L 43 GLN cc_start: 0.7873 (pt0) cc_final: 0.7575 (pt0) REVERT: A 423 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8154 (mp) REVERT: A 455 MET cc_start: 0.7700 (tmm) cc_final: 0.7341 (ttp) REVERT: A 497 TYR cc_start: 0.6908 (m-80) cc_final: 0.6654 (m-80) REVERT: A 610 TRP cc_start: 0.6891 (t60) cc_final: 0.6689 (t60) outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.0839 time to fit residues: 13.1368 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 472 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.179025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153397 restraints weight = 9928.348| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.11 r_work: 0.3752 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8137 Z= 0.117 Angle : 0.549 10.389 11064 Z= 0.274 Chirality : 0.041 0.190 1184 Planarity : 0.004 0.051 1410 Dihedral : 4.317 58.870 1062 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.07 % Allowed : 12.34 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.38 (0.27), residues: 962 helix: 0.87 (0.27), residues: 375 sheet: 0.35 (0.42), residues: 148 loop : -0.21 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 46 TYR 0.015 0.001 TYR A 50 PHE 0.010 0.001 PHE E 456 TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8122) covalent geometry : angle 0.54380 / 0.27 (11027) SS BOND : bond 0.00233 / 0.12 ( 8) SS BOND : angle 0.86009 / 0.49 ( 16) hydrogen bonds : bond 0.03957 / 2.69 ( 353) hydrogen bonds : angle 4.32281 / 2.95 ( 975) link_BETA1-6 : bond 0.00024 / 0.01 ( 1) link_BETA1-6 : angle 1.50334 / 0.80 ( 3) link_NAG-ASN : bond 0.00220 / 0.10 ( 6) link_NAG-ASN : angle 1.71405 / 1.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 GLN cc_start: 0.7855 (pt0) cc_final: 0.7573 (pt0) REVERT: A 423 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 455 MET cc_start: 0.7650 (tmm) cc_final: 0.7337 (ttp) REVERT: A 497 TYR cc_start: 0.6812 (m-80) cc_final: 0.6571 (m-80) REVERT: A 610 TRP cc_start: 0.6800 (t60) cc_final: 0.6588 (t60) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.0862 time to fit residues: 12.1605 Evaluate side-chains 98 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154175 restraints weight = 9882.206| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.06 r_work: 0.3750 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8137 Z= 0.110 Angle : 0.536 9.836 11064 Z= 0.268 Chirality : 0.041 0.177 1184 Planarity : 0.004 0.051 1410 Dihedral : 4.212 58.741 1062 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.95 % Allowed : 12.46 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.53 (0.27), residues: 962 helix: 1.06 (0.27), residues: 375 sheet: 0.40 (0.42), residues: 148 loop : -0.18 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 46 TYR 0.015 0.001 TYR A 50 PHE 0.010 0.001 PHE E 456 TRP 0.014 0.001 TRP A 275 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8122) covalent geometry : angle 0.53097 / 0.27 (11027) SS BOND : bond 0.00230 / 0.12 ( 8) SS BOND : angle 0.95258 / 0.52 ( 16) hydrogen bonds : bond 0.03808 / 2.60 ( 353) hydrogen bonds : angle 4.24593 / 2.90 ( 975) link_BETA1-6 : bond 0.00075 / 0.04 ( 1) link_BETA1-6 : angle 1.42153 / 0.75 ( 3) link_NAG-ASN : bond 0.00211 / 0.10 ( 6) link_NAG-ASN : angle 1.63469 / 0.97 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 GLN cc_start: 0.7885 (pt0) cc_final: 0.7618 (pt0) REVERT: A 423 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 455 MET cc_start: 0.7656 (tmm) cc_final: 0.7371 (ttp) REVERT: A 497 TYR cc_start: 0.6789 (m-80) cc_final: 0.6505 (m-80) outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 0.0785 time to fit residues: 11.4248 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.180533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.154461 restraints weight = 9964.756| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.13 r_work: 0.3733 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8137 Z= 0.130 Angle : 0.554 9.827 11064 Z= 0.277 Chirality : 0.041 0.189 1184 Planarity : 0.004 0.051 1410 Dihedral : 4.275 58.078 1062 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.07 % Allowed : 12.57 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.52 (0.27), residues: 962 helix: 0.95 (0.27), residues: 382 sheet: 0.41 (0.42), residues: 148 loop : -0.10 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 403 TYR 0.016 0.001 TYR A 50 PHE 0.012 0.001 PHE A 438 TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8122) covalent geometry : angle 0.54869 / 0.28 (11027) SS BOND : bond 0.00256 / 0.13 ( 8) SS BOND : angle 0.95194 / 0.53 ( 16) hydrogen bonds : bond 0.04087 / 2.78 ( 353) hydrogen bonds : angle 4.25569 / 2.90 ( 975) link_BETA1-6 : bond 0.00080 / 0.04 ( 1) link_BETA1-6 : angle 1.52330 / 0.81 ( 3) link_NAG-ASN : bond 0.00227 / 0.11 ( 6) link_NAG-ASN : angle 1.67233 / 0.99 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.82 seconds wall clock time: 34 minutes 7.36 seconds (2047.36 seconds total)