Starting phenix.real_space_refine on Sat May 10 12:15:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380.map" model { file = "/net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca4_45380/05_2025/9ca4_45380_neut.cif" } resolution = 3.01 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.24, per 1000 atoms: 0.68 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: 1.43 Conformation dependent library (CDL) restraints added in 772.1 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: 1.67 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: 1.62 Time building geometry restraints manager: 1.68 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=" 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' U E -1 " pdb=" P A E 0 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.50e-02 4.44e+03 6.98e+00 bond pdb=" N ASN A 71 " pdb=" CA ASN A 71 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.70e+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: 731 0.044 - 0.088: 179 0.088 - 0.131: 55 0.131 - 0.175: 10 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: 3.430 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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= 0.346 Angle : 0.870 37.956 8657 Z= 0.483 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 (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: -0.38 (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 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 60 PHE 0.018 0.002 PHE A 265 TYR 0.016 0.002 TYR A 240 ARG 0.007 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.19650 ( 250) hydrogen bonds : angle 5.89950 ( 705) covalent geometry : bond 0.00464 ( 6371) covalent geometry : angle 0.86963 ( 8657) Misc. bond : bond 0.20258 ( 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 : 0.707 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: 0.1660 time to fit residues: 46.9432 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.0050 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.123775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110027 restraints weight = 10143.568| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.56 r_work: 0.3398 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6372 Z= 0.146 Angle : 0.590 10.733 8657 Z= 0.303 Chirality : 0.044 0.237 977 Planarity : 0.005 0.061 1090 Dihedral : 8.276 73.437 940 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.90 % Allowed : 14.41 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.30), residues: 766 helix: 0.77 (0.30), residues: 292 sheet: 0.47 (0.49), residues: 128 loop : -0.88 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.002 0.001 HIS A 60 PHE 0.031 0.002 PHE A 214 TYR 0.014 0.001 TYR A 240 ARG 0.005 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 250) hydrogen bonds : angle 4.60052 ( 705) covalent geometry : bond 0.00329 ( 6371) covalent geometry : angle 0.59012 ( 8657) Misc. bond : bond 0.00005 ( 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 201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.620 Fit side-chains REVERT: A 21 LEU cc_start: 0.8385 (tp) cc_final: 0.8154 (tt) REVERT: A 48 GLN cc_start: 0.8042 (mp10) cc_final: 0.7702 (mp10) REVERT: A 56 SER cc_start: 0.8508 (p) cc_final: 0.8290 (p) REVERT: A 93 ASN cc_start: 0.8103 (t0) cc_final: 0.7855 (t0) REVERT: A 124 ASN cc_start: 0.8207 (t0) cc_final: 0.7967 (t0) REVERT: A 159 ASP cc_start: 0.7814 (m-30) cc_final: 0.7495 (t0) REVERT: A 169 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 185 ASP cc_start: 0.7777 (m-30) cc_final: 0.7532 (m-30) REVERT: A 234 SER cc_start: 0.8737 (t) cc_final: 0.8491 (p) REVERT: A 284 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7138 (mm-40) REVERT: A 306 MET cc_start: 0.8116 (ttp) cc_final: 0.7870 (ttp) REVERT: A 431 ILE cc_start: 0.8374 (mm) cc_final: 0.8162 (mt) REVERT: A 465 GLU cc_start: 0.8140 (tp30) cc_final: 0.7374 (tt0) REVERT: A 503 MET cc_start: 0.8201 (mtp) cc_final: 0.7980 (mtm) REVERT: A 526 TYR cc_start: 0.8598 (m-10) cc_final: 0.8196 (m-10) REVERT: A 530 GLU cc_start: 0.7089 (pm20) cc_final: 0.6769 (pm20) REVERT: A 569 ASN cc_start: 0.8797 (t0) cc_final: 0.8517 (t0) REVERT: A 579 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: B 156 HIS cc_start: 0.7545 (m-70) cc_final: 0.7341 (m90) outliers start: 6 outliers final: 5 residues processed: 195 average time/residue: 0.1574 time to fit residues: 40.9419 Evaluate side-chains 192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain B residue 62 VAL 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 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109555 restraints weight = 10147.116| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.59 r_work: 0.3393 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1632 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= 0.150 Angle : 0.555 9.677 8657 Z= 0.285 Chirality : 0.042 0.163 977 Planarity : 0.005 0.058 1090 Dihedral : 7.981 73.166 940 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.25 % Allowed : 15.32 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.30), residues: 766 helix: 0.84 (0.31), residues: 294 sheet: 0.58 (0.49), residues: 127 loop : -0.82 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 415 PHE 0.026 0.002 PHE A 235 TYR 0.014 0.001 TYR A 426 ARG 0.004 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 250) hydrogen bonds : angle 4.42417 ( 705) covalent geometry : bond 0.00342 ( 6371) covalent geometry : angle 0.55493 ( 8657) Misc. bond : bond 0.00086 ( 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 207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.8447 (tp) cc_final: 0.8238 (tt) REVERT: A 48 GLN cc_start: 0.8026 (mp10) cc_final: 0.7609 (mp10) REVERT: A 56 SER cc_start: 0.8534 (p) cc_final: 0.8327 (p) REVERT: A 124 ASN cc_start: 0.8213 (t0) cc_final: 0.7978 (t0) REVERT: A 159 ASP cc_start: 0.7856 (m-30) cc_final: 0.7543 (t0) REVERT: A 185 ASP cc_start: 0.7820 (m-30) cc_final: 0.7475 (m-30) REVERT: A 234 SER cc_start: 0.8728 (t) cc_final: 0.8431 (p) REVERT: A 284 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7229 (mm-40) REVERT: A 404 ASP cc_start: 0.8037 (m-30) cc_final: 0.7754 (t0) REVERT: A 431 ILE cc_start: 0.8392 (mm) cc_final: 0.8184 (mt) REVERT: A 465 GLU cc_start: 0.8129 (tp30) cc_final: 0.7681 (tm-30) REVERT: A 526 TYR cc_start: 0.8600 (m-10) cc_final: 0.8181 (m-10) REVERT: A 530 GLU cc_start: 0.7124 (pm20) cc_final: 0.6912 (pm20) REVERT: A 569 ASN cc_start: 0.8749 (t0) cc_final: 0.8476 (t0) REVERT: A 579 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7617 (mmm-85) REVERT: B 156 HIS cc_start: 0.7591 (m-70) cc_final: 0.7330 (m90) outliers start: 15 outliers final: 14 residues processed: 193 average time/residue: 0.1660 time to fit residues: 42.6737 Evaluate side-chains 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 96 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 370 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 439 LEU 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 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 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 49 optimal weight: 0.0170 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 74 optimal weight: 0.0980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.124437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110507 restraints weight = 10189.012| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.62 r_work: 0.3403 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6372 Z= 0.118 Angle : 0.529 11.145 8657 Z= 0.269 Chirality : 0.041 0.210 977 Planarity : 0.004 0.054 1090 Dihedral : 7.768 73.177 940 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.95 % Allowed : 17.27 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.31), residues: 766 helix: 0.97 (0.31), residues: 292 sheet: 0.42 (0.47), residues: 134 loop : -0.82 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS A 415 PHE 0.029 0.002 PHE A 214 TYR 0.012 0.001 TYR A 240 ARG 0.005 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 250) hydrogen bonds : angle 4.24950 ( 705) covalent geometry : bond 0.00264 ( 6371) covalent geometry : angle 0.52927 ( 8657) Misc. bond : bond 0.00002 ( 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 207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7984 (mp10) cc_final: 0.7588 (mp10) REVERT: A 124 ASN cc_start: 0.8229 (t0) cc_final: 0.7982 (t0) REVERT: A 159 ASP cc_start: 0.7898 (m-30) cc_final: 0.7568 (t0) REVERT: A 169 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 185 ASP cc_start: 0.7786 (m-30) cc_final: 0.7451 (m-30) REVERT: A 232 ILE cc_start: 0.8616 (mm) cc_final: 0.8295 (tp) REVERT: A 234 SER cc_start: 0.8724 (t) cc_final: 0.8396 (p) REVERT: A 284 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7243 (mm-40) REVERT: A 296 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7547 (mt0) REVERT: A 404 ASP cc_start: 0.8014 (m-30) cc_final: 0.7760 (t0) REVERT: A 431 ILE cc_start: 0.8366 (mm) cc_final: 0.8164 (mt) REVERT: A 505 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8526 (ttmm) REVERT: A 526 TYR cc_start: 0.8581 (m-10) cc_final: 0.8182 (m-10) REVERT: A 530 GLU cc_start: 0.7141 (pm20) cc_final: 0.6906 (pm20) REVERT: A 552 ASP cc_start: 0.7718 (t0) cc_final: 0.7433 (t0) REVERT: A 579 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7587 (mmm-85) REVERT: B 156 HIS cc_start: 0.7585 (m-70) cc_final: 0.7331 (m90) outliers start: 13 outliers final: 10 residues processed: 197 average time/residue: 0.1589 time to fit residues: 42.3650 Evaluate side-chains 196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 478 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 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.123249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109512 restraints weight = 10208.960| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.61 r_work: 0.3384 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6372 Z= 0.164 Angle : 0.550 10.913 8657 Z= 0.281 Chirality : 0.042 0.187 977 Planarity : 0.004 0.053 1090 Dihedral : 7.780 73.014 940 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.25 % Allowed : 18.02 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.30), residues: 766 helix: 0.88 (0.31), residues: 294 sheet: 0.40 (0.47), residues: 134 loop : -0.74 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 415 PHE 0.019 0.002 PHE A 214 TYR 0.016 0.002 TYR A 240 ARG 0.004 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 250) hydrogen bonds : angle 4.28386 ( 705) covalent geometry : bond 0.00377 ( 6371) covalent geometry : angle 0.55004 ( 8657) Misc. bond : bond 0.00016 ( 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 202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.640 Fit side-chains REVERT: A 48 GLN cc_start: 0.7947 (mp10) cc_final: 0.7729 (mp10) REVERT: A 159 ASP cc_start: 0.7899 (m-30) cc_final: 0.7569 (t0) REVERT: A 162 ASN cc_start: 0.7600 (t0) cc_final: 0.7271 (t0) REVERT: A 185 ASP cc_start: 0.7783 (m-30) cc_final: 0.7436 (m-30) REVERT: A 234 SER cc_start: 0.8734 (t) cc_final: 0.8398 (p) REVERT: A 284 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7285 (mm-40) REVERT: A 285 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8140 (m) REVERT: A 306 MET cc_start: 0.7996 (ttp) cc_final: 0.7763 (ttp) REVERT: A 404 ASP cc_start: 0.8045 (m-30) cc_final: 0.7801 (t0) REVERT: A 431 ILE cc_start: 0.8372 (mm) cc_final: 0.8170 (mt) REVERT: A 505 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8514 (ttmm) REVERT: A 526 TYR cc_start: 0.8575 (m-10) cc_final: 0.8162 (m-10) REVERT: A 530 GLU cc_start: 0.7096 (pm20) cc_final: 0.6795 (pm20) REVERT: A 569 ASN cc_start: 0.8748 (t0) cc_final: 0.8371 (t0) REVERT: A 579 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7596 (mmm-85) REVERT: B 156 HIS cc_start: 0.7580 (m-70) cc_final: 0.7326 (m90) outliers start: 15 outliers final: 11 residues processed: 191 average time/residue: 0.1727 time to fit residues: 43.5908 Evaluate side-chains 198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 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 439 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 59 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.0050 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.124242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110532 restraints weight = 10201.582| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.59 r_work: 0.3410 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2123 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= 0.119 Angle : 0.548 11.931 8657 Z= 0.273 Chirality : 0.041 0.206 977 Planarity : 0.004 0.064 1090 Dihedral : 7.714 73.147 940 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.70 % Allowed : 19.82 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.31), residues: 766 helix: 0.98 (0.31), residues: 292 sheet: 0.42 (0.47), residues: 134 loop : -0.73 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS A 415 PHE 0.023 0.001 PHE A 214 TYR 0.013 0.001 TYR A 240 ARG 0.004 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 250) hydrogen bonds : angle 4.16217 ( 705) covalent geometry : bond 0.00270 ( 6371) covalent geometry : angle 0.54848 ( 8657) Misc. bond : bond 0.00005 ( 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 207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7907 (mp10) cc_final: 0.7483 (mp10) REVERT: A 93 ASN cc_start: 0.8168 (t0) cc_final: 0.7775 (t0) REVERT: A 159 ASP cc_start: 0.7907 (m-30) cc_final: 0.7544 (t0) REVERT: A 162 ASN cc_start: 0.7575 (t0) cc_final: 0.7237 (t0) REVERT: A 185 ASP cc_start: 0.7761 (m-30) cc_final: 0.7412 (m-30) REVERT: A 234 SER cc_start: 0.8715 (t) cc_final: 0.8390 (p) REVERT: A 284 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7282 (mm-40) REVERT: A 285 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8154 (m) REVERT: A 404 ASP cc_start: 0.7994 (m-30) cc_final: 0.7748 (t0) REVERT: A 431 ILE cc_start: 0.8357 (mm) cc_final: 0.8150 (mt) REVERT: A 505 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8532 (ttmm) REVERT: A 526 TYR cc_start: 0.8569 (m-10) cc_final: 0.8176 (m-10) REVERT: A 530 GLU cc_start: 0.7116 (pm20) cc_final: 0.6808 (pm20) REVERT: A 569 ASN cc_start: 0.8741 (t0) cc_final: 0.8359 (t0) REVERT: A 579 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.7567 (mmm-85) REVERT: B 156 HIS cc_start: 0.7572 (m-70) cc_final: 0.7314 (m90) outliers start: 18 outliers final: 12 residues processed: 195 average time/residue: 0.1766 time to fit residues: 45.9779 Evaluate side-chains 201 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 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 119 LEU Chi-restraints excluded: chain B residue 133 VAL 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 51 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.125178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111434 restraints weight = 10238.904| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.61 r_work: 0.3422 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6372 Z= 0.111 Angle : 0.539 12.055 8657 Z= 0.269 Chirality : 0.041 0.200 977 Planarity : 0.004 0.061 1090 Dihedral : 7.633 73.168 940 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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 (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: 0.30 (0.31), residues: 766 helix: 1.08 (0.31), residues: 292 sheet: 0.50 (0.47), residues: 134 loop : -0.65 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS A 60 PHE 0.028 0.002 PHE A 235 TYR 0.012 0.001 TYR A 240 ARG 0.002 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 250) hydrogen bonds : angle 4.10571 ( 705) covalent geometry : bond 0.00251 ( 6371) covalent geometry : angle 0.53939 ( 8657) Misc. bond : bond 0.00003 ( 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 200 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7883 (mp10) cc_final: 0.7458 (mp10) REVERT: A 54 MET cc_start: 0.7998 (ttt) cc_final: 0.7666 (ttt) REVERT: A 93 ASN cc_start: 0.8169 (t0) cc_final: 0.7773 (t0) REVERT: A 134 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 159 ASP cc_start: 0.7876 (m-30) cc_final: 0.7531 (t0) REVERT: A 162 ASN cc_start: 0.7564 (t0) cc_final: 0.7227 (t0) REVERT: A 185 ASP cc_start: 0.7730 (m-30) cc_final: 0.7367 (m-30) REVERT: A 234 SER cc_start: 0.8709 (t) cc_final: 0.8348 (p) REVERT: A 284 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7369 (mm-40) REVERT: A 285 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8149 (m) REVERT: A 306 MET cc_start: 0.8019 (ttp) cc_final: 0.7768 (ttp) REVERT: A 404 ASP cc_start: 0.8038 (m-30) cc_final: 0.7791 (t0) REVERT: A 431 ILE cc_start: 0.8357 (mm) cc_final: 0.8155 (mt) REVERT: A 505 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8495 (ttmm) REVERT: A 526 TYR cc_start: 0.8572 (m-10) cc_final: 0.8242 (m-10) REVERT: A 530 GLU cc_start: 0.7174 (pm20) cc_final: 0.6878 (pm20) REVERT: A 569 ASN cc_start: 0.8744 (t0) cc_final: 0.8346 (t0) REVERT: A 579 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7570 (mmm-85) REVERT: B 156 HIS cc_start: 0.7467 (m-70) cc_final: 0.7198 (m90) outliers start: 18 outliers final: 12 residues processed: 187 average time/residue: 0.1663 time to fit residues: 41.6674 Evaluate side-chains 192 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 134 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 119 LEU Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.123912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110145 restraints weight = 10184.179| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.62 r_work: 0.3399 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2309 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= 0.148 Angle : 0.553 12.493 8657 Z= 0.279 Chirality : 0.042 0.186 977 Planarity : 0.004 0.058 1090 Dihedral : 7.610 73.063 940 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.70 % Allowed : 20.87 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.31), residues: 766 helix: 0.99 (0.31), residues: 294 sheet: 0.44 (0.47), residues: 134 loop : -0.62 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 406 HIS 0.003 0.001 HIS A 415 PHE 0.028 0.002 PHE A 235 TYR 0.015 0.001 TYR A 240 ARG 0.007 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 250) hydrogen bonds : angle 4.15653 ( 705) covalent geometry : bond 0.00340 ( 6371) covalent geometry : angle 0.55346 ( 8657) Misc. bond : bond 0.00011 ( 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 198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7889 (mp10) cc_final: 0.7455 (mp10) REVERT: A 54 MET cc_start: 0.8004 (ttt) cc_final: 0.7649 (ttt) REVERT: A 93 ASN cc_start: 0.8190 (t0) cc_final: 0.7785 (t0) REVERT: A 145 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7776 (tttt) REVERT: A 159 ASP cc_start: 0.7881 (m-30) cc_final: 0.7556 (t0) REVERT: A 162 ASN cc_start: 0.7590 (t0) cc_final: 0.7132 (t0) REVERT: A 185 ASP cc_start: 0.7781 (m-30) cc_final: 0.7424 (m-30) REVERT: A 234 SER cc_start: 0.8722 (t) cc_final: 0.8362 (p) REVERT: A 284 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7389 (mm-40) REVERT: A 285 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8159 (m) REVERT: A 306 MET cc_start: 0.7972 (ttp) cc_final: 0.7729 (ttp) REVERT: A 404 ASP cc_start: 0.8076 (m-30) cc_final: 0.7827 (t0) REVERT: A 431 ILE cc_start: 0.8354 (mm) cc_final: 0.8149 (mt) REVERT: A 505 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8515 (ttmm) REVERT: A 526 TYR cc_start: 0.8616 (m-10) cc_final: 0.8301 (m-10) REVERT: A 530 GLU cc_start: 0.7116 (pm20) cc_final: 0.6808 (pm20) REVERT: A 569 ASN cc_start: 0.8772 (t0) cc_final: 0.8356 (t0) REVERT: A 575 LYS cc_start: 0.8774 (mttt) cc_final: 0.8471 (mttm) REVERT: A 579 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7631 (mmm-85) REVERT: B 111 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: B 156 HIS cc_start: 0.7521 (m-70) cc_final: 0.7283 (m-70) outliers start: 18 outliers final: 13 residues processed: 186 average time/residue: 0.1857 time to fit residues: 45.7349 Evaluate side-chains 194 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 111 PHE 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 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 66 optimal weight: 0.0040 chunk 50 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.0616 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.127391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.113435 restraints weight = 10395.857| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.67 r_work: 0.3464 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6372 Z= 0.095 Angle : 0.546 12.346 8657 Z= 0.272 Chirality : 0.040 0.209 977 Planarity : 0.004 0.068 1090 Dihedral : 7.615 73.345 940 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.65 % Allowed : 21.92 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.31), residues: 766 helix: 1.08 (0.31), residues: 302 sheet: 0.59 (0.48), residues: 134 loop : -0.62 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.002 0.000 HIS A 172 PHE 0.023 0.001 PHE A 235 TYR 0.011 0.001 TYR A 411 ARG 0.007 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 250) hydrogen bonds : angle 3.93494 ( 705) covalent geometry : bond 0.00206 ( 6371) covalent geometry : angle 0.54576 ( 8657) Misc. bond : bond 0.00001 ( 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 193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7883 (mp10) cc_final: 0.7455 (mp10) REVERT: A 54 MET cc_start: 0.7926 (ttt) cc_final: 0.7574 (ttt) REVERT: A 93 ASN cc_start: 0.8154 (t0) cc_final: 0.7770 (t0) REVERT: A 105 GLU cc_start: 0.7511 (tp30) cc_final: 0.7212 (tp30) REVERT: A 134 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 159 ASP cc_start: 0.7828 (m-30) cc_final: 0.7486 (t0) REVERT: A 162 ASN cc_start: 0.7526 (t0) cc_final: 0.7171 (t0) REVERT: A 185 ASP cc_start: 0.7634 (m-30) cc_final: 0.7266 (m-30) REVERT: A 234 SER cc_start: 0.8676 (t) cc_final: 0.8307 (p) REVERT: A 284 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7479 (mm-40) REVERT: A 285 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 404 ASP cc_start: 0.7993 (m-30) cc_final: 0.7624 (t0) REVERT: A 431 ILE cc_start: 0.8299 (mm) cc_final: 0.8087 (mt) REVERT: A 526 TYR cc_start: 0.8563 (m-10) cc_final: 0.8225 (m-10) REVERT: A 530 GLU cc_start: 0.7163 (pm20) cc_final: 0.6932 (pm20) REVERT: A 569 ASN cc_start: 0.8738 (t0) cc_final: 0.8319 (t0) REVERT: A 575 LYS cc_start: 0.8695 (mttt) cc_final: 0.8380 (mttm) REVERT: A 579 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7424 (mmm-85) outliers start: 11 outliers final: 9 residues processed: 184 average time/residue: 0.1857 time to fit residues: 45.6728 Evaluate side-chains 188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 227 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.124108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110329 restraints weight = 10345.911| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.66 r_work: 0.3396 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6372 Z= 0.168 Angle : 0.586 12.455 8657 Z= 0.295 Chirality : 0.043 0.184 977 Planarity : 0.005 0.069 1090 Dihedral : 7.609 73.056 940 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.65 % Allowed : 22.07 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.29 (0.31), residues: 766 helix: 1.02 (0.31), residues: 298 sheet: 0.46 (0.47), residues: 134 loop : -0.61 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 406 HIS 0.003 0.001 HIS A 415 PHE 0.027 0.002 PHE A 235 TYR 0.014 0.002 TYR A 240 ARG 0.007 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 250) hydrogen bonds : angle 4.12964 ( 705) covalent geometry : bond 0.00389 ( 6371) covalent geometry : angle 0.58568 ( 8657) Misc. bond : bond 0.00032 ( 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 193 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 48 GLN cc_start: 0.7840 (mp10) cc_final: 0.7379 (mp10) REVERT: A 54 MET cc_start: 0.8001 (ttt) cc_final: 0.7651 (ttt) REVERT: A 93 ASN cc_start: 0.8194 (t0) cc_final: 0.7804 (t0) REVERT: A 105 GLU cc_start: 0.7553 (tp30) cc_final: 0.7256 (tp30) REVERT: A 134 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8645 (mp) REVERT: A 159 ASP cc_start: 0.7871 (m-30) cc_final: 0.7542 (t0) REVERT: A 162 ASN cc_start: 0.7558 (t0) cc_final: 0.7102 (t0) REVERT: A 185 ASP cc_start: 0.7815 (m-30) cc_final: 0.7464 (m-30) REVERT: A 234 SER cc_start: 0.8716 (t) cc_final: 0.8356 (p) REVERT: A 284 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7412 (mm-40) REVERT: A 285 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8184 (m) REVERT: A 404 ASP cc_start: 0.8140 (m-30) cc_final: 0.7859 (t0) REVERT: A 431 ILE cc_start: 0.8356 (mm) cc_final: 0.8152 (mt) REVERT: A 526 TYR cc_start: 0.8628 (m-10) cc_final: 0.8298 (m-10) REVERT: A 530 GLU cc_start: 0.7183 (pm20) cc_final: 0.6871 (pm20) REVERT: A 569 ASN cc_start: 0.8763 (t0) cc_final: 0.8374 (t0) REVERT: A 575 LYS cc_start: 0.8741 (mttt) cc_final: 0.8418 (mttm) REVERT: A 579 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7630 (mmm-85) outliers start: 11 outliers final: 8 residues processed: 186 average time/residue: 0.1820 time to fit residues: 44.6567 Evaluate side-chains 191 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 478 VAL 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 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 20 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.122792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109281 restraints weight = 10370.771| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.64 r_work: 0.3380 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6372 Z= 0.189 Angle : 0.605 12.507 8657 Z= 0.305 Chirality : 0.044 0.214 977 Planarity : 0.005 0.067 1090 Dihedral : 7.717 75.709 940 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.80 % Allowed : 22.52 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.31), residues: 766 helix: 0.82 (0.30), residues: 299 sheet: 0.28 (0.46), residues: 134 loop : -0.63 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 406 HIS 0.003 0.001 HIS A 415 PHE 0.029 0.002 PHE A 235 TYR 0.017 0.002 TYR A 240 ARG 0.007 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 250) hydrogen bonds : angle 4.25734 ( 705) covalent geometry : bond 0.00435 ( 6371) covalent geometry : angle 0.60493 ( 8657) Misc. bond : bond 0.00031 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.35 seconds wall clock time: 56 minutes 46.17 seconds (3406.17 seconds total)