Starting phenix.real_space_refine on Tue Aug 4 19:02:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca4_45380/08_2026/9ca4_45380_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca4_45380/08_2026/9ca4_45380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ca4_45380/08_2026/9ca4_45380_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca4_45380/08_2026/9ca4_45380_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ca4_45380/08_2026/9ca4_45380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca4_45380/08_2026/9ca4_45380.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 8 5.49 5 S 39 5.16 5 C 3905 2.51 5 N 1076 2.21 5 O 1200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6230 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4843 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Classifications: {'RNA': 2} Modifications used: {'5*END': 1, 'rna2p_pyr': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.08, per 1000 atoms: 0.17 Number of scatterers: 6230 At special positions: 0 Unit cell: (73.87, 87.98, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 39 16.00 P 8 15.00 O 1200 8.00 N 1076 7.00 C 3905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 294.0 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 42.6% alpha, 16.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.858A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 204 removed outlier: 4.253A pdb=" N ALA A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.620A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 357 through 360 removed outlier: 3.602A pdb=" N HIS A 360 " --> pdb=" O GLN A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.565A pdb=" N ALA A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.561A pdb=" N LEU A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.746A pdb=" N ARG A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.743A pdb=" N GLU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.727A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 removed outlier: 4.221A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.756A pdb=" N VAL A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 4.570A pdb=" N LEU A 557 " --> pdb=" O GLU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 removed outlier: 4.198A pdb=" N SER A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.737A pdb=" N LYS A 592 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.873A pdb=" N ASP A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.577A pdb=" N THR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 43 removed outlier: 4.530A pdb=" N LEU B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 removed outlier: 3.553A pdb=" N ASN B 146 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 147 " --> pdb=" O ASP B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 143 through 147' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.627A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 449 removed outlier: 6.904A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 245 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP A 259 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A 243 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 480 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN A 248 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL A 478 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 476 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 430 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 530 Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.499A pdb=" N ASP B 134 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU B 140 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LYS B 126 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.61 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1728 1.33 - 1.45: 1037 1.45 - 1.57: 3531 1.57 - 1.69: 13 1.69 - 1.81: 62 Bond restraints: 6371 Sorted by residual: bond pdb=" OH PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.769 1.608 0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.23e+01 bond pdb=" O3' U E -1 " pdb=" P A E 0 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.20e-02 6.94e+03 1.09e+01 bond pdb=" N GLU A 465 " pdb=" CA GLU A 465 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.57e+00 bond pdb=" O3' A E 1 " pdb=" P A E 2 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.20e-02 6.94e+03 6.47e+00 ... (remaining 6366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.59: 8650 7.59 - 15.18: 4 15.18 - 22.77: 1 22.77 - 30.36: 0 30.36 - 37.96: 2 Bond angle restraints: 8657 Sorted by residual: angle pdb=" O SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 123.00 85.04 37.96 1.60e+00 3.91e-01 5.63e+02 angle pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 116.20 149.47 -33.27 2.00e+00 2.50e-01 2.77e+02 angle pdb=" C SER A 335 " pdb=" N PTR A 336 " pdb=" CA PTR A 336 " ideal model delta sigma weight residual 121.70 138.72 -17.02 1.80e+00 3.09e-01 8.94e+01 angle pdb=" C GLU A 465 " pdb=" N SER A 466 " pdb=" CA SER A 466 " ideal model delta sigma weight residual 122.95 114.97 7.98 1.44e+00 4.82e-01 3.07e+01 angle pdb=" C ASN A 71 " pdb=" CA ASN A 71 " pdb=" CB ASN A 71 " ideal model delta sigma weight residual 110.42 101.56 8.86 1.99e+00 2.53e-01 1.98e+01 ... (remaining 8652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3423 17.54 - 35.08: 344 35.08 - 52.61: 79 52.61 - 70.15: 15 70.15 - 87.69: 5 Dihedral angle restraints: 3866 sinusoidal: 1632 harmonic: 2234 Sorted by residual: dihedral pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " pdb=" CA PTR A 336 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" O4' A E 0 " pdb=" C2' A E 0 " pdb=" C1' A E 0 " pdb=" C3' A E 0 " ideal model delta sinusoidal sigma weight residual 25.00 -1.81 26.81 1 8.00e+00 1.56e-02 1.61e+01 dihedral pdb=" C4' A E 0 " pdb=" O4' A E 0 " pdb=" C1' A E 0 " pdb=" C2' A E 0 " ideal model delta sinusoidal sigma weight residual 3.00 -22.17 25.17 1 8.00e+00 1.56e-02 1.42e+01 ... (remaining 3863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 730 0.044 - 0.088: 179 0.088 - 0.131: 58 0.131 - 0.175: 8 0.175 - 0.219: 2 Chirality restraints: 977 Sorted by residual: chirality pdb=" C3' A E 0 " pdb=" C4' A E 0 " pdb=" O3' A E 0 " pdb=" C2' A E 0 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU A 134 " pdb=" N LEU A 134 " pdb=" C LEU A 134 " pdb=" CB LEU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" C3' A E 1 " pdb=" C4' A E 1 " pdb=" O3' A E 1 " pdb=" C2' A E 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 974 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 335 " 0.048 2.00e-02 2.50e+03 6.95e-02 4.83e+01 pdb=" C SER A 335 " -0.120 2.00e-02 2.50e+03 pdb=" O SER A 335 " 0.028 2.00e-02 2.50e+03 pdb=" N PTR A 336 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 456 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO A 457 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 464 " -0.015 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C GLU A 464 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU A 464 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU A 465 " -0.016 2.00e-02 2.50e+03 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 85 2.65 - 3.21: 5606 3.21 - 3.78: 8814 3.78 - 4.34: 11790 4.34 - 4.90: 19739 Nonbonded interactions: 46034 Sorted by model distance: nonbonded pdb=" OE2 GLU A 9 " pdb="MN MN A 702 " model vdw 2.091 2.320 nonbonded pdb=" OE2 GLU A 340 " pdb=" OD2 ASP A 511 " model vdw 2.114 3.040 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 702 " model vdw 2.164 2.320 nonbonded pdb=" OD2 ASP A 511 " pdb="MN MN A 701 " model vdw 2.168 2.320 nonbonded pdb=" O ASP A 185 " pdb=" O2' U E -1 " model vdw 2.199 3.040 ... (remaining 46029 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: 2.370 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.005 0.203 6372 Z= 0.353 Angle : 0.871 37.956 8657 Z= 0.486 Chirality : 0.044 0.219 977 Planarity : 0.006 0.077 1090 Dihedral : 14.819 87.692 2424 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.30), residues: 766 helix: 0.35 (0.30), residues: 291 sheet: 0.26 (0.48), residues: 137 loop : -0.93 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 434 TYR 0.016 0.002 TYR A 240 PHE 0.018 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.25 ( 6371) covalent geometry : angle 0.87126 / 0.49 ( 8657) hydrogen bonds : bond 0.19650 / 13.25 ( 250) hydrogen bonds : angle 5.89950 / 4.04 ( 705) Misc. bond : bond 0.20258 / 10.66 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 93 ASN cc_start: 0.7593 (t0) cc_final: 0.7389 (t0) REVERT: A 185 ASP cc_start: 0.7302 (m-30) cc_final: 0.7096 (m-30) REVERT: A 285 VAL cc_start: 0.8386 (p) cc_final: 0.8097 (m) REVERT: A 431 ILE cc_start: 0.8354 (mm) cc_final: 0.8136 (mt) REVERT: A 505 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8304 (ttpp) REVERT: A 528 THR cc_start: 0.7886 (p) cc_final: 0.7465 (p) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0607 time to fit residues: 17.7844 Evaluate side-chains 204 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.0470 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110867 restraints weight = 10209.796| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.57 r_work: 0.3412 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6372 Z= 0.136 Angle : 0.607 10.591 8657 Z= 0.313 Chirality : 0.042 0.155 977 Planarity : 0.005 0.059 1090 Dihedral : 8.372 73.510 940 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.90 % Allowed : 14.11 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.30), residues: 766 helix: 0.68 (0.30), residues: 292 sheet: 0.44 (0.49), residues: 128 loop : -0.89 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.014 0.001 TYR A 426 PHE 0.028 0.002 PHE A 214 TRP 0.009 0.001 TRP A 458 HIS 0.002 0.000 HIS A 584 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 6371) covalent geometry : angle 0.60736 / 0.31 ( 8657) hydrogen bonds : bond 0.05867 / 3.96 ( 250) hydrogen bonds : angle 4.74984 / 3.22 ( 705) Misc. bond : bond 0.00193 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8066 (mp10) cc_final: 0.7723 (mp10) REVERT: A 93 ASN cc_start: 0.8019 (t0) cc_final: 0.7712 (t0) REVERT: A 110 ASP cc_start: 0.7881 (t70) cc_final: 0.7676 (t0) REVERT: A 124 ASN cc_start: 0.8217 (t0) cc_final: 0.7966 (t0) REVERT: A 159 ASP cc_start: 0.7787 (m-30) cc_final: 0.7491 (t0) REVERT: A 185 ASP cc_start: 0.7689 (m-30) cc_final: 0.7453 (m-30) REVERT: A 234 SER cc_start: 0.8759 (t) cc_final: 0.8512 (p) REVERT: A 284 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7057 (mm-40) REVERT: A 306 MET cc_start: 0.8132 (ttp) cc_final: 0.7878 (ttp) REVERT: A 431 ILE cc_start: 0.8378 (mm) cc_final: 0.8152 (mt) REVERT: A 579 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7678 (mmm-85) outliers start: 6 outliers final: 4 residues processed: 194 average time/residue: 0.0534 time to fit residues: 14.2298 Evaluate side-chains 199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 195 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.0040 chunk 76 optimal weight: 0.2980 overall best weight: 0.2910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 347 ASN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.124822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.110890 restraints weight = 10150.255| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.61 r_work: 0.3415 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6372 Z= 0.122 Angle : 0.563 9.938 8657 Z= 0.291 Chirality : 0.042 0.139 977 Planarity : 0.005 0.059 1090 Dihedral : 8.169 73.451 940 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.65 % Allowed : 15.32 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.30), residues: 766 helix: 0.83 (0.31), residues: 292 sheet: 0.46 (0.48), residues: 128 loop : -0.86 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.011 0.001 TYR A 240 PHE 0.025 0.001 PHE A 235 TRP 0.017 0.001 TRP A 241 HIS 0.001 0.000 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6371) covalent geometry : angle 0.56280 / 0.29 ( 8657) hydrogen bonds : bond 0.04924 / 3.34 ( 250) hydrogen bonds : angle 4.53276 / 3.06 ( 705) Misc. bond : bond 0.00121 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.151 Fit side-chains REVERT: A 159 ASP cc_start: 0.7814 (m-30) cc_final: 0.7504 (t0) REVERT: A 185 ASP cc_start: 0.7756 (m-30) cc_final: 0.7464 (m-30) REVERT: A 234 SER cc_start: 0.8730 (t) cc_final: 0.8424 (p) REVERT: A 284 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7086 (mm-40) REVERT: A 404 ASP cc_start: 0.8025 (m-30) cc_final: 0.7747 (t0) REVERT: A 431 ILE cc_start: 0.8357 (mm) cc_final: 0.8141 (mt) REVERT: A 465 GLU cc_start: 0.8085 (tp30) cc_final: 0.7635 (tm-30) REVERT: A 526 TYR cc_start: 0.8571 (m-10) cc_final: 0.8149 (m-10) REVERT: A 530 GLU cc_start: 0.6855 (pm20) cc_final: 0.6556 (pm20) REVERT: A 569 ASN cc_start: 0.8801 (t0) cc_final: 0.8527 (t0) REVERT: A 579 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7520 (mmm-85) outliers start: 11 outliers final: 7 residues processed: 186 average time/residue: 0.0532 time to fit residues: 13.3886 Evaluate side-chains 187 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.122839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109011 restraints weight = 10201.694| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.59 r_work: 0.3387 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6372 Z= 0.177 Angle : 0.554 9.363 8657 Z= 0.289 Chirality : 0.043 0.147 977 Planarity : 0.005 0.064 1090 Dihedral : 8.013 73.148 940 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.25 % Allowed : 16.22 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.30), residues: 766 helix: 0.78 (0.31), residues: 294 sheet: 0.29 (0.48), residues: 132 loop : -0.81 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 151 TYR 0.016 0.002 TYR A 426 PHE 0.024 0.002 PHE A 235 TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 6371) covalent geometry : angle 0.55379 / 0.29 ( 8657) hydrogen bonds : bond 0.05065 / 3.48 ( 250) hydrogen bonds : angle 4.50317 / 3.04 ( 705) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.167 Fit side-chains REVERT: A 124 ASN cc_start: 0.8226 (t0) cc_final: 0.8009 (t0) REVERT: A 159 ASP cc_start: 0.7849 (m-30) cc_final: 0.7530 (t0) REVERT: A 185 ASP cc_start: 0.7774 (m-30) cc_final: 0.7454 (m-30) REVERT: A 234 SER cc_start: 0.8735 (t) cc_final: 0.8412 (p) REVERT: A 250 ASP cc_start: 0.8221 (m-30) cc_final: 0.8001 (m-30) REVERT: A 284 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7235 (mm-40) REVERT: A 404 ASP cc_start: 0.8046 (m-30) cc_final: 0.7781 (t0) REVERT: A 431 ILE cc_start: 0.8397 (mm) cc_final: 0.8187 (mt) REVERT: A 503 MET cc_start: 0.8219 (mtp) cc_final: 0.7981 (mtm) REVERT: A 530 GLU cc_start: 0.7089 (pm20) cc_final: 0.6729 (pm20) REVERT: A 569 ASN cc_start: 0.8781 (t0) cc_final: 0.8446 (t0) REVERT: A 579 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7526 (mmm-85) REVERT: A 592 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8361 (mmtp) outliers start: 15 outliers final: 13 residues processed: 196 average time/residue: 0.0591 time to fit residues: 15.6706 Evaluate side-chains 202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 0.0070 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.123579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109753 restraints weight = 10367.602| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.64 r_work: 0.3393 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6372 Z= 0.125 Angle : 0.545 10.923 8657 Z= 0.279 Chirality : 0.041 0.138 977 Planarity : 0.005 0.064 1090 Dihedral : 7.935 73.237 940 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.70 % Allowed : 16.67 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.30), residues: 766 helix: 0.86 (0.31), residues: 292 sheet: 0.37 (0.48), residues: 134 loop : -0.80 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.014 0.001 TYR A 240 PHE 0.028 0.002 PHE A 214 TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6371) covalent geometry : angle 0.54488 / 0.28 ( 8657) hydrogen bonds : bond 0.04579 / 3.13 ( 250) hydrogen bonds : angle 4.37545 / 2.95 ( 705) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8133 (t0) cc_final: 0.7700 (t0) REVERT: A 124 ASN cc_start: 0.8237 (t0) cc_final: 0.7998 (t0) REVERT: A 159 ASP cc_start: 0.7863 (m-30) cc_final: 0.7538 (t0) REVERT: A 185 ASP cc_start: 0.7778 (m-30) cc_final: 0.7440 (m-30) REVERT: A 234 SER cc_start: 0.8742 (t) cc_final: 0.8406 (p) REVERT: A 284 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7242 (mm-40) REVERT: A 285 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8130 (m) REVERT: A 404 ASP cc_start: 0.8059 (m-30) cc_final: 0.7796 (t0) REVERT: A 431 ILE cc_start: 0.8373 (mm) cc_final: 0.8155 (mt) REVERT: A 465 GLU cc_start: 0.7955 (tp30) cc_final: 0.7381 (tt0) REVERT: A 503 MET cc_start: 0.8200 (mtp) cc_final: 0.7973 (mtm) REVERT: A 526 TYR cc_start: 0.8588 (m-10) cc_final: 0.8167 (m-10) REVERT: A 530 GLU cc_start: 0.7126 (pm20) cc_final: 0.6764 (pm20) REVERT: A 569 ASN cc_start: 0.8764 (t0) cc_final: 0.8508 (t0) REVERT: A 579 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7528 (mmm-85) outliers start: 18 outliers final: 14 residues processed: 195 average time/residue: 0.0554 time to fit residues: 14.7898 Evaluate side-chains 202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109607 restraints weight = 10241.852| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.62 r_work: 0.3393 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6372 Z= 0.145 Angle : 0.544 10.522 8657 Z= 0.278 Chirality : 0.042 0.138 977 Planarity : 0.004 0.059 1090 Dihedral : 7.876 73.133 940 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.00 % Allowed : 17.12 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.30), residues: 766 helix: 0.82 (0.31), residues: 294 sheet: 0.36 (0.47), residues: 134 loop : -0.77 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 151 TYR 0.014 0.001 TYR A 240 PHE 0.017 0.001 PHE A 235 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 6371) covalent geometry : angle 0.54418 / 0.28 ( 8657) hydrogen bonds : bond 0.04608 / 3.15 ( 250) hydrogen bonds : angle 4.33337 / 2.91 ( 705) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.146 Fit side-chains REVERT: A 93 ASN cc_start: 0.8149 (t0) cc_final: 0.7719 (t0) REVERT: A 124 ASN cc_start: 0.8243 (t0) cc_final: 0.8001 (t0) REVERT: A 159 ASP cc_start: 0.7884 (m-30) cc_final: 0.7547 (t0) REVERT: A 185 ASP cc_start: 0.7797 (m-30) cc_final: 0.7440 (m-30) REVERT: A 234 SER cc_start: 0.8732 (t) cc_final: 0.8382 (p) REVERT: A 284 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7252 (mm-40) REVERT: A 285 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8112 (m) REVERT: A 404 ASP cc_start: 0.8062 (m-30) cc_final: 0.7798 (t0) REVERT: A 431 ILE cc_start: 0.8364 (mm) cc_final: 0.8154 (mt) REVERT: A 465 GLU cc_start: 0.8075 (tp30) cc_final: 0.7835 (tp30) REVERT: A 503 MET cc_start: 0.8220 (mtp) cc_final: 0.8013 (mtm) REVERT: A 526 TYR cc_start: 0.8605 (m-10) cc_final: 0.8197 (m-10) REVERT: A 530 GLU cc_start: 0.7109 (pm20) cc_final: 0.6786 (pm20) REVERT: A 569 ASN cc_start: 0.8755 (t0) cc_final: 0.8470 (t0) REVERT: A 579 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7496 (mmm-85) REVERT: B 156 HIS cc_start: 0.7622 (m90) cc_final: 0.7349 (m90) outliers start: 20 outliers final: 16 residues processed: 186 average time/residue: 0.0503 time to fit residues: 12.8776 Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.122535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.108783 restraints weight = 10218.392| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.59 r_work: 0.3383 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6372 Z= 0.172 Angle : 0.564 11.710 8657 Z= 0.288 Chirality : 0.043 0.142 977 Planarity : 0.005 0.067 1090 Dihedral : 7.859 72.986 940 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.85 % Allowed : 17.87 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.30), residues: 766 helix: 0.78 (0.30), residues: 294 sheet: 0.36 (0.47), residues: 134 loop : -0.77 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.016 0.002 TYR A 240 PHE 0.018 0.002 PHE A 265 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 6371) covalent geometry : angle 0.56449 / 0.29 ( 8657) hydrogen bonds : bond 0.04804 / 3.30 ( 250) hydrogen bonds : angle 4.34900 / 2.93 ( 705) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.166 Fit side-chains REVERT: A 93 ASN cc_start: 0.8164 (t0) cc_final: 0.7731 (t0) REVERT: A 124 ASN cc_start: 0.8274 (t0) cc_final: 0.8003 (t0) REVERT: A 159 ASP cc_start: 0.7904 (m-30) cc_final: 0.7564 (t0) REVERT: A 185 ASP cc_start: 0.7784 (m-30) cc_final: 0.7438 (m-30) REVERT: A 234 SER cc_start: 0.8747 (t) cc_final: 0.8398 (p) REVERT: A 284 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7288 (mm-40) REVERT: A 285 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8117 (m) REVERT: A 404 ASP cc_start: 0.8080 (m-30) cc_final: 0.7812 (t0) REVERT: A 431 ILE cc_start: 0.8381 (mm) cc_final: 0.8173 (mt) REVERT: A 465 GLU cc_start: 0.8093 (tp30) cc_final: 0.7870 (tp30) REVERT: A 505 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8532 (ttmm) REVERT: A 526 TYR cc_start: 0.8578 (m-10) cc_final: 0.8224 (m-10) REVERT: A 530 GLU cc_start: 0.7121 (pm20) cc_final: 0.6873 (pm20) REVERT: B 156 HIS cc_start: 0.7658 (m90) cc_final: 0.7409 (m90) outliers start: 19 outliers final: 14 residues processed: 194 average time/residue: 0.0580 time to fit residues: 15.0344 Evaluate side-chains 198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108472 restraints weight = 10273.337| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.63 r_work: 0.3376 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6372 Z= 0.191 Angle : 0.579 12.002 8657 Z= 0.295 Chirality : 0.043 0.144 977 Planarity : 0.005 0.066 1090 Dihedral : 7.869 72.947 940 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.85 % Allowed : 19.52 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.30), residues: 766 helix: 0.80 (0.30), residues: 294 sheet: 0.36 (0.47), residues: 134 loop : -0.80 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.019 0.002 TYR A 240 PHE 0.033 0.002 PHE A 214 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 6371) covalent geometry : angle 0.57916 / 0.30 ( 8657) hydrogen bonds : bond 0.04949 / 3.40 ( 250) hydrogen bonds : angle 4.34638 / 2.93 ( 705) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.198 Fit side-chains REVERT: A 54 MET cc_start: 0.8033 (ttt) cc_final: 0.7639 (ttt) REVERT: A 93 ASN cc_start: 0.8161 (t0) cc_final: 0.7738 (t0) REVERT: A 159 ASP cc_start: 0.7932 (m-30) cc_final: 0.7578 (t0) REVERT: A 162 ASN cc_start: 0.7582 (t0) cc_final: 0.7282 (t0) REVERT: A 185 ASP cc_start: 0.7812 (m-30) cc_final: 0.7467 (m-30) REVERT: A 234 SER cc_start: 0.8763 (t) cc_final: 0.8424 (p) REVERT: A 284 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7302 (mm-40) REVERT: A 285 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8119 (m) REVERT: A 404 ASP cc_start: 0.8104 (m-30) cc_final: 0.7859 (t0) REVERT: A 431 ILE cc_start: 0.8368 (mm) cc_final: 0.8167 (mt) REVERT: A 505 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8529 (ttmm) REVERT: A 526 TYR cc_start: 0.8639 (m-10) cc_final: 0.8309 (m-10) REVERT: A 530 GLU cc_start: 0.7134 (pm20) cc_final: 0.6885 (pm20) REVERT: A 569 ASN cc_start: 0.8754 (t0) cc_final: 0.8364 (t0) REVERT: B 156 HIS cc_start: 0.7685 (m90) cc_final: 0.7420 (m90) outliers start: 19 outliers final: 16 residues processed: 190 average time/residue: 0.0582 time to fit residues: 14.9389 Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.122677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108900 restraints weight = 10231.589| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.59 r_work: 0.3383 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6372 Z= 0.165 Angle : 0.585 12.683 8657 Z= 0.296 Chirality : 0.042 0.142 977 Planarity : 0.005 0.070 1090 Dihedral : 7.853 73.011 940 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.55 % Allowed : 20.42 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.30), residues: 766 helix: 0.81 (0.30), residues: 294 sheet: 0.34 (0.47), residues: 134 loop : -0.78 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.019 0.002 TYR A 240 PHE 0.020 0.002 PHE A 152 TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6371) covalent geometry : angle 0.58543 / 0.30 ( 8657) hydrogen bonds : bond 0.04777 / 3.28 ( 250) hydrogen bonds : angle 4.32543 / 2.91 ( 705) Misc. bond : bond 0.00000 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.8028 (ttt) cc_final: 0.7639 (ttt) REVERT: A 93 ASN cc_start: 0.8162 (t0) cc_final: 0.7737 (t0) REVERT: A 159 ASP cc_start: 0.7917 (m-30) cc_final: 0.7573 (t0) REVERT: A 162 ASN cc_start: 0.7584 (t0) cc_final: 0.7288 (t0) REVERT: A 185 ASP cc_start: 0.7811 (m-30) cc_final: 0.7460 (m-30) REVERT: A 234 SER cc_start: 0.8755 (t) cc_final: 0.8405 (p) REVERT: A 284 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7294 (mm-40) REVERT: A 285 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8113 (m) REVERT: A 306 MET cc_start: 0.8051 (ttp) cc_final: 0.7791 (ttp) REVERT: A 404 ASP cc_start: 0.8113 (m-30) cc_final: 0.7868 (t0) REVERT: A 431 ILE cc_start: 0.8373 (mm) cc_final: 0.8170 (mt) REVERT: A 505 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8523 (ttmm) REVERT: A 526 TYR cc_start: 0.8642 (m-10) cc_final: 0.8311 (m-10) REVERT: A 530 GLU cc_start: 0.7123 (pm20) cc_final: 0.6922 (pm20) REVERT: A 569 ASN cc_start: 0.8749 (t0) cc_final: 0.8355 (t0) REVERT: B 156 HIS cc_start: 0.7673 (m90) cc_final: 0.7392 (m90) outliers start: 17 outliers final: 15 residues processed: 188 average time/residue: 0.0574 time to fit residues: 14.4401 Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 38 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109993 restraints weight = 10176.292| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.59 r_work: 0.3399 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6372 Z= 0.126 Angle : 0.573 12.955 8657 Z= 0.289 Chirality : 0.041 0.176 977 Planarity : 0.005 0.068 1090 Dihedral : 7.774 73.103 940 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.70 % Allowed : 20.72 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.30), residues: 766 helix: 0.88 (0.31), residues: 294 sheet: 0.38 (0.47), residues: 134 loop : -0.76 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 369 TYR 0.016 0.001 TYR A 240 PHE 0.016 0.001 PHE A 152 TRP 0.009 0.001 TRP A 458 HIS 0.002 0.000 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6371) covalent geometry : angle 0.57275 / 0.29 ( 8657) hydrogen bonds : bond 0.04434 / 3.01 ( 250) hydrogen bonds : angle 4.26970 / 2.87 ( 705) Misc. bond : bond 0.00015 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.8014 (ttt) cc_final: 0.7632 (ttt) REVERT: A 93 ASN cc_start: 0.8149 (t0) cc_final: 0.7729 (t0) REVERT: A 159 ASP cc_start: 0.7910 (m-30) cc_final: 0.7572 (t0) REVERT: A 162 ASN cc_start: 0.7569 (t0) cc_final: 0.7272 (t0) REVERT: A 164 MET cc_start: 0.8529 (tpp) cc_final: 0.7649 (tpp) REVERT: A 185 ASP cc_start: 0.7790 (m-30) cc_final: 0.7422 (m-30) REVERT: A 234 SER cc_start: 0.8734 (t) cc_final: 0.8388 (p) REVERT: A 284 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7299 (mm-40) REVERT: A 285 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8154 (m) REVERT: A 306 MET cc_start: 0.8056 (ttp) cc_final: 0.7822 (ttt) REVERT: A 404 ASP cc_start: 0.8078 (m-30) cc_final: 0.7823 (t0) REVERT: A 431 ILE cc_start: 0.8359 (mm) cc_final: 0.8153 (mt) REVERT: A 505 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8528 (ttmm) REVERT: A 526 TYR cc_start: 0.8614 (m-10) cc_final: 0.8307 (m-10) REVERT: A 530 GLU cc_start: 0.7126 (pm20) cc_final: 0.6904 (pm20) REVERT: A 569 ASN cc_start: 0.8741 (t0) cc_final: 0.8345 (t0) REVERT: B 156 HIS cc_start: 0.7648 (m90) cc_final: 0.7373 (m90) outliers start: 18 outliers final: 15 residues processed: 184 average time/residue: 0.0613 time to fit residues: 14.9603 Evaluate side-chains 198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.122901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109159 restraints weight = 10216.735| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.60 r_work: 0.3387 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6372 Z= 0.172 Angle : 0.595 12.663 8657 Z= 0.302 Chirality : 0.043 0.206 977 Planarity : 0.005 0.068 1090 Dihedral : 7.782 72.980 940 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.10 % Allowed : 21.32 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.30), residues: 766 helix: 0.83 (0.30), residues: 294 sheet: 0.38 (0.47), residues: 134 loop : -0.75 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 151 TYR 0.019 0.002 TYR A 240 PHE 0.029 0.002 PHE A 235 TRP 0.026 0.002 TRP A 241 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6371) covalent geometry : angle 0.59463 / 0.30 ( 8657) hydrogen bonds : bond 0.04771 / 3.25 ( 250) hydrogen bonds : angle 4.36276 / 2.94 ( 705) Misc. bond : bond 0.00003 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1276.27 seconds wall clock time: 22 minutes 34.83 seconds (1354.83 seconds total)