Starting phenix.real_space_refine on Wed Mar 12 14:54:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxb_29530/03_2025/8fxb_29530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxb_29530/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxb_29530/03_2025/8fxb_29530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxb_29530/03_2025/8fxb_29530.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxb_29530/03_2025/8fxb_29530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxb_29530/03_2025/8fxb_29530.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.77, per 1000 atoms: 0.60 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: 1.94 Conformation dependent library (CDL) restraints added in 839.1 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: 0.97 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: 2.36 Time building geometry restraints manager: 2.30 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: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- 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 0.059 8122 Z= 0.721 Angle : 1.210 12.604 11027 Z= 0.841 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.003 TRP H 117 HIS 0.004 0.001 HIS A 378 PHE 0.021 0.003 PHE L 98 TYR 0.031 0.004 TYR E 495 ARG 0.003 0.000 ARG A 177 *********************** 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 : 0.780 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: 0.1730 time to fit residues: 42.5461 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 : 0.787 ------------------------------------------------------------------------------- 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 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** 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 = 0.4219 r_free = 0.4219 target = 0.185725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161539 restraints weight = 9635.723| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.03 r_work: 0.3830 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8122 Z= 0.191 Angle : 0.565 7.809 11027 Z= 0.300 Chirality : 0.042 0.170 1184 Planarity : 0.005 0.064 1410 Dihedral : 5.155 57.474 1212 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 962 helix: 0.51 (0.27), residues: 382 sheet: 0.66 (0.40), residues: 149 loop : 0.14 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 275 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.006 0.001 ARG A 177 *********************** 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 132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.802 Fit side-chains REVERT: L 24 ARG cc_start: 0.6344 (mmm-85) cc_final: 0.6100 (tpp80) REVERT: H 43 GLN cc_start: 0.7386 (mm110) cc_final: 0.7039 (tt0) REVERT: A 95 LEU cc_start: 0.6278 (pp) cc_final: 0.4839 (tp) REVERT: A 111 ASP cc_start: 0.7278 (t0) cc_final: 0.6816 (m-30) REVERT: A 441 LYS cc_start: 0.7237 (tttt) cc_final: 0.7024 (ttpt) REVERT: A 455 MET cc_start: 0.7596 (tmm) cc_final: 0.7050 (ttp) outliers start: 8 outliers final: 4 residues processed: 128 average time/residue: 0.2036 time to fit residues: 35.9920 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 : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain A residue 107 VAL 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 57 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.153525 restraints weight = 9926.943| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.04 r_work: 0.3733 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 8122 Z= 0.296 Angle : 0.604 6.188 11027 Z= 0.316 Chirality : 0.044 0.172 1184 Planarity : 0.005 0.056 1410 Dihedral : 4.804 57.699 1205 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.30 % Allowed : 8.66 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 962 helix: 0.41 (0.27), residues: 375 sheet: 0.58 (0.41), residues: 148 loop : 0.05 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 117 HIS 0.005 0.001 HIS A 378 PHE 0.017 0.002 PHE A 438 TYR 0.028 0.002 TYR E 365 ARG 0.004 0.001 ARG A 460 *********************** 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 118 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.786 Fit side-chains REVERT: L 24 ARG cc_start: 0.6648 (mmm-85) cc_final: 0.6398 (tpp80) REVERT: A 106 SER cc_start: 0.6220 (m) cc_final: 0.5996 (p) REVERT: A 423 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7916 (mp) REVERT: A 441 LYS cc_start: 0.7408 (tttt) cc_final: 0.7129 (ttpt) REVERT: A 455 MET cc_start: 0.7701 (tmm) cc_final: 0.7334 (ttp) outliers start: 11 outliers final: 5 residues processed: 115 average time/residue: 0.1886 time to fit residues: 30.2085 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 491 VAL 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 16 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 228 HIS E 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.181050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155794 restraints weight = 9864.904| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.07 r_work: 0.3765 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8122 Z= 0.168 Angle : 0.527 8.253 11027 Z= 0.269 Chirality : 0.041 0.151 1184 Planarity : 0.004 0.053 1410 Dihedral : 4.519 57.668 1205 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.54 % Allowed : 9.13 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 962 helix: 0.69 (0.27), residues: 375 sheet: 0.44 (0.41), residues: 149 loop : 0.15 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 228 PHE 0.010 0.001 PHE A 438 TYR 0.012 0.001 TYR E 495 ARG 0.002 0.000 ARG A 460 *********************** 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 125 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.862 Fit side-chains REVERT: L 24 ARG cc_start: 0.6453 (mmm-85) cc_final: 0.6204 (tpp80) REVERT: H 43 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7206 (tt0) REVERT: H 82 GLU cc_start: 0.7768 (tt0) cc_final: 0.7536 (tt0) REVERT: A 166 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6429 (tm-30) REVERT: A 423 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 441 LYS cc_start: 0.7369 (tttt) cc_final: 0.7127 (ttpt) REVERT: A 455 MET cc_start: 0.7609 (tmm) cc_final: 0.7342 (ttp) REVERT: A 470 LYS cc_start: 0.7808 (mttt) cc_final: 0.7491 (tttt) outliers start: 13 outliers final: 7 residues processed: 121 average time/residue: 0.1879 time to fit residues: 31.8272 Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 468 ILE 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 45 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 210 ASN A 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.175464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150483 restraints weight = 9822.407| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.99 r_work: 0.3704 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 8122 Z= 0.371 Angle : 0.651 8.241 11027 Z= 0.332 Chirality : 0.046 0.203 1184 Planarity : 0.005 0.055 1410 Dihedral : 5.100 59.326 1205 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.66 % Allowed : 10.44 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 962 helix: 0.28 (0.27), residues: 373 sheet: 0.43 (0.41), residues: 147 loop : -0.02 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 477 HIS 0.005 0.002 HIS A 378 PHE 0.021 0.002 PHE A 438 TYR 0.023 0.002 TYR E 495 ARG 0.004 0.001 ARG A 460 *********************** 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 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6597 (mmm-85) cc_final: 0.6344 (tpp80) REVERT: H 43 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7216 (tt0) REVERT: H 82 GLU cc_start: 0.7825 (tt0) cc_final: 0.7616 (tt0) REVERT: A 106 SER cc_start: 0.6204 (m) cc_final: 0.5993 (p) REVERT: A 126 ILE cc_start: 0.7066 (mt) cc_final: 0.6844 (mt) REVERT: A 166 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6543 (tm-30) REVERT: A 423 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8007 (mp) REVERT: A 441 LYS cc_start: 0.7507 (tttt) cc_final: 0.7150 (ttpt) REVERT: A 455 MET cc_start: 0.7718 (tmm) cc_final: 0.7324 (ttp) REVERT: A 610 TRP cc_start: 0.6567 (t60) cc_final: 0.6301 (t60) outliers start: 14 outliers final: 11 residues processed: 113 average time/residue: 0.1878 time to fit residues: 29.7178 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 433 GLU Chi-restraints excluded: chain A residue 468 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 210 ASN A 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.177320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152105 restraints weight = 9857.381| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.05 r_work: 0.3724 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8122 Z= 0.221 Angle : 0.566 8.935 11027 Z= 0.286 Chirality : 0.042 0.188 1184 Planarity : 0.004 0.052 1410 Dihedral : 4.873 59.821 1205 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.66 % Allowed : 10.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 962 helix: 0.53 (0.27), residues: 375 sheet: 0.47 (0.41), residues: 147 loop : -0.03 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.003 0.001 HIS A 228 PHE 0.013 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.003 0.000 ARG A 460 *********************** 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: 14 poor density : 102 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: L 24 ARG cc_start: 0.6514 (mmm-85) cc_final: 0.6284 (tpp80) REVERT: A 166 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6503 (tm-30) REVERT: A 255 TYR cc_start: 0.7396 (m-80) cc_final: 0.7182 (m-10) REVERT: A 423 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 441 LYS cc_start: 0.7532 (tttt) cc_final: 0.7100 (ttpt) REVERT: A 455 MET cc_start: 0.7676 (tmm) cc_final: 0.7318 (ttp) REVERT: A 610 TRP cc_start: 0.6733 (t60) cc_final: 0.6474 (t60) outliers start: 14 outliers final: 9 residues processed: 111 average time/residue: 0.2003 time to fit residues: 30.9415 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 : 1.198 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 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 210 ASN A 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.179700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154395 restraints weight = 9909.694| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.07 r_work: 0.3752 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8122 Z= 0.162 Angle : 0.513 8.690 11027 Z= 0.261 Chirality : 0.040 0.159 1184 Planarity : 0.004 0.050 1410 Dihedral : 4.548 59.720 1205 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.66 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 962 helix: 0.76 (0.27), residues: 376 sheet: 0.49 (0.42), residues: 148 loop : 0.06 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.002 0.001 HIS A 374 PHE 0.009 0.001 PHE E 456 TYR 0.016 0.001 TYR A 50 ARG 0.003 0.000 ARG L 46 *********************** 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 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 GLU cc_start: 0.7859 (tt0) cc_final: 0.7574 (tt0) REVERT: A 166 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6490 (tm-30) REVERT: A 255 TYR cc_start: 0.7344 (m-80) cc_final: 0.7130 (m-10) REVERT: A 423 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 441 LYS cc_start: 0.7449 (tttt) cc_final: 0.7003 (ttpt) REVERT: A 455 MET cc_start: 0.7648 (tmm) cc_final: 0.7365 (ttp) REVERT: A 610 TRP cc_start: 0.6773 (t60) cc_final: 0.6506 (t60) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.1821 time to fit residues: 28.8806 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 : 0.777 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.177931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.152381 restraints weight = 10049.962| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.10 r_work: 0.3731 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8122 Z= 0.228 Angle : 0.560 8.246 11027 Z= 0.284 Chirality : 0.042 0.178 1184 Planarity : 0.004 0.051 1410 Dihedral : 4.735 59.536 1205 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.42 % Allowed : 12.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 962 helix: 0.69 (0.27), residues: 375 sheet: 0.46 (0.42), residues: 147 loop : -0.01 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.002 PHE A 438 TYR 0.017 0.002 TYR E 495 ARG 0.004 0.000 ARG L 46 *********************** 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 112 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 GLN cc_start: 0.7893 (pt0) cc_final: 0.7600 (pt0) REVERT: H 62 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: H 82 GLU cc_start: 0.7858 (tt0) cc_final: 0.7591 (tt0) REVERT: A 166 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6405 (tm-30) REVERT: A 423 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8087 (mp) REVERT: A 441 LYS cc_start: 0.7467 (tttt) cc_final: 0.6936 (ttpt) REVERT: A 455 MET cc_start: 0.7661 (tmm) cc_final: 0.7294 (ttp) REVERT: A 610 TRP cc_start: 0.6806 (t60) cc_final: 0.6562 (t60) outliers start: 12 outliers final: 9 residues processed: 108 average time/residue: 0.1810 time to fit residues: 27.8936 Evaluate side-chains 109 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 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 90 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.177261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151982 restraints weight = 10157.184| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.07 r_work: 0.3723 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8122 Z= 0.226 Angle : 0.564 8.591 11027 Z= 0.286 Chirality : 0.042 0.183 1184 Planarity : 0.004 0.050 1410 Dihedral : 4.767 59.144 1205 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.42 % Allowed : 12.34 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.27), residues: 962 helix: 0.65 (0.27), residues: 381 sheet: 0.46 (0.42), residues: 147 loop : -0.02 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 477 HIS 0.003 0.001 HIS L 92 PHE 0.013 0.001 PHE A 438 TYR 0.015 0.002 TYR A 41 ARG 0.004 0.000 ARG L 46 *********************** 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 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 GLN cc_start: 0.7943 (pt0) cc_final: 0.7656 (pt0) REVERT: H 82 GLU cc_start: 0.7855 (tt0) cc_final: 0.7580 (tt0) REVERT: A 166 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6520 (tm-30) REVERT: A 423 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 441 LYS cc_start: 0.7490 (tttt) cc_final: 0.7003 (ttpt) REVERT: A 455 MET cc_start: 0.7697 (tmm) cc_final: 0.7334 (ttp) REVERT: A 610 TRP cc_start: 0.6872 (t60) cc_final: 0.6651 (t60) outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 0.1969 time to fit residues: 30.0575 Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.0070 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.179185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154122 restraints weight = 9805.326| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.04 r_work: 0.3746 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8122 Z= 0.164 Angle : 0.532 8.618 11027 Z= 0.269 Chirality : 0.041 0.165 1184 Planarity : 0.004 0.049 1410 Dihedral : 4.584 59.572 1205 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.07 % Allowed : 12.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 962 helix: 0.95 (0.27), residues: 375 sheet: 0.44 (0.43), residues: 148 loop : -0.04 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.010 0.001 PHE E 456 TYR 0.012 0.001 TYR E 351 ARG 0.004 0.000 ARG L 46 ********************** 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 108 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 GLN cc_start: 0.7928 (pt0) cc_final: 0.7647 (pt0) REVERT: H 82 GLU cc_start: 0.7874 (tt0) cc_final: 0.7600 (tt0) REVERT: A 166 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6455 (tm-30) REVERT: A 423 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 441 LYS cc_start: 0.7456 (tttt) cc_final: 0.6944 (ttpt) REVERT: A 455 MET cc_start: 0.7658 (tmm) cc_final: 0.7371 (ttp) REVERT: A 610 TRP cc_start: 0.6874 (t60) cc_final: 0.6651 (t60) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.2184 time to fit residues: 32.3800 Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 472 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.177083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151839 restraints weight = 9951.846| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.06 r_work: 0.3720 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8122 Z= 0.232 Angle : 0.568 8.356 11027 Z= 0.289 Chirality : 0.042 0.180 1184 Planarity : 0.004 0.050 1410 Dihedral : 4.747 58.782 1205 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.19 % Allowed : 12.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 962 helix: 0.75 (0.27), residues: 382 sheet: 0.47 (0.42), residues: 147 loop : -0.08 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.014 0.001 PHE A 438 TYR 0.016 0.002 TYR E 495 ARG 0.004 0.000 ARG L 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.88 seconds wall clock time: 63 minutes 46.63 seconds (3826.63 seconds total)