Starting phenix.real_space_refine on Fri Aug 22 21:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxb_29530/08_2025/8fxb_29530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxb_29530/08_2025/8fxb_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fxb_29530/08_2025/8fxb_29530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxb_29530/08_2025/8fxb_29530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fxb_29530/08_2025/8fxb_29530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxb_29530/08_2025/8fxb_29530.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.23, per 1000 atoms: 0.28 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: 0.70 Conformation dependent library (CDL) restraints added in 450.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.39 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: 1.40 Time building geometry restraints manager: 0.93 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: 4497 12.97 - 25.94: 243 25.94 - 38.91: 70 38.91 - 51.88: 28 51.88 - 64.85: 23 Dihedral angle restraints: 4861 sinusoidal: 2028 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 4858 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: 0.010 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 10.518 64.853 3025 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 aren 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 covalent geometry : bond 0.01119 ( 8122) covalent geometry : angle 1.20953 (11027) SS BOND : bond 0.02926 ( 8) SS BOND : angle 4.41897 ( 16) hydrogen bonds : bond 0.20275 ( 353) hydrogen bonds : angle 7.09615 ( 975) link_BETA1-6 : bond 0.04865 ( 1) link_BETA1-6 : angle 2.96652 ( 3) link_NAG-ASN : bond 0.04037 ( 6) link_NAG-ASN : angle 5.65421 ( 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 : 0.400 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: 0.0807 time to fit residues: 20.0792 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 : 0.299 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 43 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.186704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162448 restraints weight = 9758.014| |-----------------------------------------------------------------------------| r_work (start): 0.3990 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: 0.7042 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8137 Z= 0.131 Angle : 0.562 7.520 11064 Z= 0.299 Chirality : 0.042 0.166 1184 Planarity : 0.004 0.066 1410 Dihedral : 5.141 56.439 1212 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.95 % Allowed : 7.59 % Favored : 91.46 % 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 aren not related in a simple way. whole: 0.46 (0.27), residues: 962 helix: 0.50 (0.27), residues: 384 sheet: 0.70 (0.40), residues: 150 loop : 0.16 (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 A 385 PHE 0.010 0.001 PHE E 456 TRP 0.014 0.001 TRP A 275 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8122) covalent geometry : angle 0.55592 (11027) SS BOND : bond 0.00435 ( 8) SS BOND : angle 1.15542 ( 16) hydrogen bonds : bond 0.05310 ( 353) hydrogen bonds : angle 4.99324 ( 975) link_BETA1-6 : bond 0.00595 ( 1) link_BETA1-6 : angle 1.54387 ( 3) link_NAG-ASN : bond 0.00439 ( 6) link_NAG-ASN : angle 1.74399 ( 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 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7377 (mm110) cc_final: 0.6984 (tt0) REVERT: A 95 LEU cc_start: 0.6286 (pp) cc_final: 0.4905 (tp) REVERT: A 111 ASP cc_start: 0.7279 (t0) cc_final: 0.6827 (m-30) REVERT: A 401 HIS cc_start: 0.8983 (OUTLIER) cc_final: 0.8704 (t70) REVERT: A 455 MET cc_start: 0.7623 (tmm) cc_final: 0.7278 (ttp) outliers start: 8 outliers final: 3 residues processed: 122 average time/residue: 0.0899 time to fit residues: 15.2466 Evaluate side-chains 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 228 HIS A 394 ASN A 524 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150528 restraints weight = 10009.784| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.10 r_work: 0.3705 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 8137 Z= 0.265 Angle : 0.706 6.842 11064 Z= 0.365 Chirality : 0.048 0.211 1184 Planarity : 0.006 0.064 1410 Dihedral : 5.438 59.118 1207 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.07 % Allowed : 9.13 % Favored : 89.80 % 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 aren not related in a simple way. whole: 0.01 (0.27), residues: 962 helix: 0.11 (0.26), residues: 371 sheet: 0.49 (0.40), residues: 148 loop : -0.09 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 460 TYR 0.025 0.003 TYR E 495 PHE 0.024 0.003 PHE A 438 TRP 0.018 0.002 TRP H 117 HIS 0.008 0.002 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 8122) covalent geometry : angle 0.69973 (11027) SS BOND : bond 0.00728 ( 8) SS BOND : angle 1.56813 ( 16) hydrogen bonds : bond 0.05982 ( 353) hydrogen bonds : angle 4.94692 ( 975) link_BETA1-6 : bond 0.00381 ( 1) link_BETA1-6 : angle 1.92163 ( 3) link_NAG-ASN : bond 0.00433 ( 6) link_NAG-ASN : angle 1.87349 ( 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 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.309 Fit side-chains REVERT: L 24 ARG cc_start: 0.6723 (mmm-85) cc_final: 0.6438 (tpp80) REVERT: H 43 GLN cc_start: 0.7796 (mm110) cc_final: 0.7369 (tt0) REVERT: A 106 SER cc_start: 0.6109 (m) cc_final: 0.5865 (p) REVERT: A 126 ILE cc_start: 0.7349 (mt) cc_final: 0.7129 (mt) REVERT: A 394 ASN cc_start: 0.8522 (m110) cc_final: 0.8264 (m-40) REVERT: A 423 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7965 (mp) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.0902 time to fit residues: 14.6427 Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL 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 544 ILE 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: 0.4980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 228 HIS A 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.168859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143157 restraints weight = 10275.543| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.16 r_work: 0.3596 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8137 Z= 0.264 Angle : 0.706 9.661 11064 Z= 0.359 Chirality : 0.048 0.235 1184 Planarity : 0.006 0.061 1410 Dihedral : 5.543 58.032 1205 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.02 % Allowed : 10.68 % 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 aren not related in a simple way. whole: -0.27 (0.26), residues: 962 helix: -0.11 (0.26), residues: 374 sheet: 0.26 (0.40), residues: 147 loop : -0.23 (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 E 495 PHE 0.023 0.003 PHE A 438 TRP 0.021 0.002 TRP A 275 HIS 0.006 0.002 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 8122) covalent geometry : angle 0.69949 (11027) SS BOND : bond 0.00531 ( 8) SS BOND : angle 1.38215 ( 16) hydrogen bonds : bond 0.05702 ( 353) hydrogen bonds : angle 4.90394 ( 975) link_BETA1-6 : bond 0.00498 ( 1) link_BETA1-6 : angle 1.85363 ( 3) link_NAG-ASN : bond 0.00372 ( 6) link_NAG-ASN : angle 2.18471 ( 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 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6671 (mmm-85) cc_final: 0.6356 (tpp80) REVERT: H 43 GLN cc_start: 0.7723 (mm110) cc_final: 0.7346 (tt0) REVERT: H 82 GLU cc_start: 0.7905 (tt0) cc_final: 0.7655 (tt0) REVERT: A 106 SER cc_start: 0.6152 (m) cc_final: 0.5911 (p) REVERT: A 126 ILE cc_start: 0.7093 (mt) cc_final: 0.6877 (mt) REVERT: A 423 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 610 TRP cc_start: 0.6715 (t60) cc_final: 0.6486 (t60) outliers start: 17 outliers final: 10 residues processed: 118 average time/residue: 0.0910 time to fit residues: 15.1191 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 385 TYR 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 544 ILE Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 472 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 101 GLN A 228 HIS E 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.178574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153136 restraints weight = 10066.701| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.12 r_work: 0.3743 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8137 Z= 0.118 Angle : 0.548 9.490 11064 Z= 0.275 Chirality : 0.041 0.183 1184 Planarity : 0.004 0.056 1410 Dihedral : 4.857 58.432 1205 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.19 % Allowed : 11.39 % Favored : 87.43 % 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 aren not related in a simple way. whole: 0.20 (0.27), residues: 962 helix: 0.50 (0.27), residues: 370 sheet: 0.29 (0.41), residues: 148 loop : -0.09 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.013 0.001 TYR E 351 PHE 0.010 0.001 PHE E 456 TRP 0.019 0.001 TRP A 275 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8122) covalent geometry : angle 0.54199 (11027) SS BOND : bond 0.00270 ( 8) SS BOND : angle 0.87866 ( 16) hydrogen bonds : bond 0.04205 ( 353) hydrogen bonds : angle 4.54973 ( 975) link_BETA1-6 : bond 0.00014 ( 1) link_BETA1-6 : angle 1.53284 ( 3) link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 1.89538 ( 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: 10 poor density : 106 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6413 (mmm-85) cc_final: 0.6123 (tpp80) REVERT: H 43 GLN cc_start: 0.7589 (mm110) cc_final: 0.7276 (tt0) REVERT: H 82 GLU cc_start: 0.7967 (tt0) cc_final: 0.7732 (tt0) REVERT: A 255 TYR cc_start: 0.7445 (m-80) cc_final: 0.7152 (m-10) REVERT: A 423 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7988 (mp) REVERT: A 455 MET cc_start: 0.7642 (tmm) cc_final: 0.7316 (ttp) REVERT: A 610 TRP cc_start: 0.6748 (t60) cc_final: 0.6504 (t60) outliers start: 10 outliers final: 5 residues processed: 113 average time/residue: 0.0942 time to fit residues: 14.7076 Evaluate side-chains 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 468 ILE 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: 3.9990 chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 228 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.166905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140849 restraints weight = 10354.958| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.19 r_work: 0.3576 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 8137 Z= 0.318 Angle : 0.753 10.896 11064 Z= 0.381 Chirality : 0.050 0.266 1184 Planarity : 0.006 0.063 1410 Dihedral : 5.792 55.039 1205 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.54 % Allowed : 12.46 % Favored : 86.00 % 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 aren not related in a simple way. whole: -0.37 (0.26), residues: 962 helix: -0.16 (0.25), residues: 382 sheet: 0.13 (0.40), residues: 147 loop : -0.28 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 460 TYR 0.028 0.003 TYR A 587 PHE 0.026 0.003 PHE A 438 TRP 0.019 0.003 TRP A 477 HIS 0.006 0.002 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00764 ( 8122) covalent geometry : angle 0.74701 (11027) SS BOND : bond 0.00553 ( 8) SS BOND : angle 1.24219 ( 16) hydrogen bonds : bond 0.06075 ( 353) hydrogen bonds : angle 4.96579 ( 975) link_BETA1-6 : bond 0.00492 ( 1) link_BETA1-6 : angle 1.80952 ( 3) link_NAG-ASN : bond 0.00464 ( 6) link_NAG-ASN : angle 2.26502 ( 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 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6727 (mmm-85) cc_final: 0.6444 (tpp80) REVERT: H 43 GLN cc_start: 0.7703 (mm110) cc_final: 0.7430 (tt0) REVERT: A 106 SER cc_start: 0.6129 (m) cc_final: 0.5906 (p) REVERT: A 423 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7965 (mp) outliers start: 13 outliers final: 12 residues processed: 111 average time/residue: 0.0863 time to fit residues: 13.4609 Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 16 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 96 GLN A 228 HIS A 239 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.177470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152179 restraints weight = 10042.643| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.09 r_work: 0.3734 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8137 Z= 0.122 Angle : 0.558 10.100 11064 Z= 0.280 Chirality : 0.041 0.190 1184 Planarity : 0.004 0.054 1410 Dihedral : 4.884 55.237 1205 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.07 % Allowed : 13.17 % Favored : 85.77 % 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 aren not related in a simple way. whole: 0.08 (0.27), residues: 962 helix: 0.52 (0.27), residues: 375 sheet: 0.20 (0.41), residues: 148 loop : -0.28 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.013 0.001 TYR E 351 PHE 0.009 0.001 PHE E 456 TRP 0.015 0.001 TRP A 275 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8122) covalent geometry : angle 0.55155 (11027) SS BOND : bond 0.00274 ( 8) SS BOND : angle 0.78273 ( 16) hydrogen bonds : bond 0.04184 ( 353) hydrogen bonds : angle 4.57109 ( 975) link_BETA1-6 : bond 0.00096 ( 1) link_BETA1-6 : angle 1.47642 ( 3) link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 2.02217 ( 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 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7783 (mm110) cc_final: 0.7391 (tt0) REVERT: H 82 GLU cc_start: 0.8004 (tt0) cc_final: 0.7758 (tt0) REVERT: A 423 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 455 MET cc_start: 0.7801 (tmm) cc_final: 0.7420 (ttp) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.0847 time to fit residues: 13.1212 Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 425 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 52 optimal weight: 0.0470 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.174578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149243 restraints weight = 10233.303| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.09 r_work: 0.3698 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8137 Z= 0.191 Angle : 0.615 9.193 11064 Z= 0.310 Chirality : 0.044 0.206 1184 Planarity : 0.005 0.056 1410 Dihedral : 5.091 53.682 1205 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.07 % Allowed : 13.64 % Favored : 85.29 % 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 aren not related in a simple way. whole: -0.00 (0.27), residues: 962 helix: 0.35 (0.26), residues: 380 sheet: 0.28 (0.42), residues: 146 loop : -0.28 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 46 TYR 0.020 0.002 TYR E 495 PHE 0.016 0.002 PHE A 438 TRP 0.017 0.002 TRP A 477 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 8122) covalent geometry : angle 0.60975 (11027) SS BOND : bond 0.00357 ( 8) SS BOND : angle 0.90673 ( 16) hydrogen bonds : bond 0.04846 ( 353) hydrogen bonds : angle 4.62158 ( 975) link_BETA1-6 : bond 0.00417 ( 1) link_BETA1-6 : angle 1.59484 ( 3) link_NAG-ASN : bond 0.00323 ( 6) link_NAG-ASN : angle 1.97796 ( 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 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6583 (mmm-85) cc_final: 0.6289 (tpp80) REVERT: H 43 GLN cc_start: 0.7839 (mm110) cc_final: 0.7472 (tt0) REVERT: H 82 GLU cc_start: 0.7998 (tt0) cc_final: 0.7773 (tt0) REVERT: A 423 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 455 MET cc_start: 0.7833 (tmm) cc_final: 0.7408 (ttp) REVERT: A 610 TRP cc_start: 0.6806 (t60) cc_final: 0.6195 (t60) outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.0901 time to fit residues: 13.4359 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 E residue 361 CYS Chi-restraints excluded: chain E residue 456 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.0000 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.151704 restraints weight = 10029.496| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.10 r_work: 0.3733 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8137 Z= 0.130 Angle : 0.561 8.824 11064 Z= 0.281 Chirality : 0.042 0.186 1184 Planarity : 0.004 0.053 1410 Dihedral : 4.806 53.892 1205 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.19 % Allowed : 13.76 % Favored : 85.05 % 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 aren not related in a simple way. whole: 0.20 (0.27), residues: 962 helix: 0.70 (0.27), residues: 374 sheet: 0.25 (0.42), residues: 148 loop : -0.28 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 46 TYR 0.017 0.001 TYR A 50 PHE 0.011 0.001 PHE A 438 TRP 0.015 0.001 TRP A 477 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8122) covalent geometry : angle 0.55510 (11027) SS BOND : bond 0.00278 ( 8) SS BOND : angle 0.77499 ( 16) hydrogen bonds : bond 0.04209 ( 353) hydrogen bonds : angle 4.49486 ( 975) link_BETA1-6 : bond 0.00113 ( 1) link_BETA1-6 : angle 1.57081 ( 3) link_NAG-ASN : bond 0.00255 ( 6) link_NAG-ASN : angle 1.93687 ( 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 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6407 (mmm-85) cc_final: 0.6135 (tpp80) REVERT: H 43 GLN cc_start: 0.7845 (mm110) cc_final: 0.7486 (tt0) REVERT: H 82 GLU cc_start: 0.7988 (tt0) cc_final: 0.7750 (tt0) REVERT: A 423 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8104 (mp) REVERT: A 455 MET cc_start: 0.7806 (tmm) cc_final: 0.7430 (ttp) REVERT: A 610 TRP cc_start: 0.6716 (t60) cc_final: 0.6086 (t60) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.0857 time to fit residues: 12.9293 Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 ASN 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 491 VAL 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: 1.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.0000 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.177577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152217 restraints weight = 10006.580| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.11 r_work: 0.3736 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8137 Z= 0.122 Angle : 0.555 9.085 11064 Z= 0.279 Chirality : 0.041 0.175 1184 Planarity : 0.004 0.053 1410 Dihedral : 4.682 53.650 1205 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.19 % Allowed : 13.76 % Favored : 85.05 % 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 aren not related in a simple way. whole: 0.32 (0.27), residues: 962 helix: 0.81 (0.27), residues: 375 sheet: 0.31 (0.42), residues: 148 loop : -0.24 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 46 TYR 0.017 0.001 TYR A 50 PHE 0.010 0.001 PHE A 523 TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8122) covalent geometry : angle 0.54897 (11027) SS BOND : bond 0.00287 ( 8) SS BOND : angle 0.95899 ( 16) hydrogen bonds : bond 0.04075 ( 353) hydrogen bonds : angle 4.41974 ( 975) link_BETA1-6 : bond 0.00041 ( 1) link_BETA1-6 : angle 1.54681 ( 3) link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 1.83587 ( 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 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7856 (mm110) cc_final: 0.7491 (tt0) REVERT: H 82 GLU cc_start: 0.8029 (tt0) cc_final: 0.7789 (tt0) REVERT: A 423 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 455 MET cc_start: 0.7789 (tmm) cc_final: 0.7447 (ttp) REVERT: A 610 TRP cc_start: 0.6738 (t60) cc_final: 0.6131 (t60) outliers start: 10 outliers final: 9 residues processed: 103 average time/residue: 0.0853 time to fit residues: 12.5593 Evaluate side-chains 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 55 ASN 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 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: 0.4980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.180635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154321 restraints weight = 10083.016| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.17 r_work: 0.3738 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8137 Z= 0.119 Angle : 0.548 9.048 11064 Z= 0.276 Chirality : 0.041 0.169 1184 Planarity : 0.004 0.052 1410 Dihedral : 4.584 53.310 1205 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.19 % Allowed : 13.64 % Favored : 85.17 % 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 aren not related in a simple way. whole: 0.39 (0.28), residues: 962 helix: 0.94 (0.27), residues: 375 sheet: 0.31 (0.43), residues: 148 loop : -0.25 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 46 TYR 0.017 0.001 TYR A 50 PHE 0.011 0.001 PHE H 64 TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8122) covalent geometry : angle 0.54212 (11027) SS BOND : bond 0.00269 ( 8) SS BOND : angle 1.02516 ( 16) hydrogen bonds : bond 0.03996 ( 353) hydrogen bonds : angle 4.35130 ( 975) link_BETA1-6 : bond 0.00087 ( 1) link_BETA1-6 : angle 1.50052 ( 3) link_NAG-ASN : bond 0.00236 ( 6) link_NAG-ASN : angle 1.78924 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.23 seconds wall clock time: 36 minutes 21.69 seconds (2181.69 seconds total)