Starting phenix.real_space_refine on Mon Jul 28 12:58:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ply_13506/07_2025/7ply_13506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ply_13506/07_2025/7ply_13506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2025/7ply_13506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2025/7ply_13506.map" model { file = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2025/7ply_13506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2025/7ply_13506.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6471 2.51 5 N 1720 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.20, per 1000 atoms: 0.71 Number of scatterers: 10149 At special positions: 0 Unit cell: (106.7, 132, 150.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1891 8.00 N 1720 7.00 C 6471 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=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 55.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.956A pdb=" N ILE A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.683A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.321A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.255A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.127A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.114A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.741A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.549A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.620A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.526A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.581A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.195A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 127 removed outlier: 4.097A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.543A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.745A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.028A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.216A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.133A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 50 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 7.669A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 5.033A pdb=" N SER A 342 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA A 349 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 344 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.599A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.856A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 529 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2903 1.33 - 1.46: 2846 1.46 - 1.60: 4514 1.60 - 1.73: 0 1.73 - 1.86: 102 Bond restraints: 10365 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.502 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O1 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.565 1.501 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" O2 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.567 1.506 0.061 2.00e-02 2.50e+03 9.16e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.82e+00 ... (remaining 10360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 13649 2.61 - 5.22: 322 5.22 - 7.84: 19 7.84 - 10.45: 5 10.45 - 13.06: 3 Bond angle restraints: 13998 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C8 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 118.25 105.19 13.06 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 128.90 117.19 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CA GLU A 144 " pdb=" CB GLU A 144 " pdb=" CG GLU A 144 " ideal model delta sigma weight residual 114.10 106.39 7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" C1' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 111.00 100.07 10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.37 117.87 -4.50 1.34e+00 5.57e-01 1.13e+01 ... (remaining 13993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 6129 35.92 - 71.84: 100 71.84 - 107.76: 26 107.76 - 143.69: 4 143.69 - 179.61: 13 Dihedral angle restraints: 6272 sinusoidal: 2598 harmonic: 3674 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.78 148.22 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" CA GLY A 563 " pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS C 61 " pdb=" C LYS C 61 " pdb=" N ARG C 62 " pdb=" CA ARG C 62 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 6269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1236 0.078 - 0.156: 263 0.156 - 0.233: 23 0.233 - 0.311: 1 0.311 - 0.389: 2 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C3 9UE C 404 " pdb=" O 9UE C 404 " pdb=" C2 9UE C 404 " pdb=" C35 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.21 2.59 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C10 9UE C 404 " pdb=" C18 9UE C 404 " pdb=" C9 9UE C 404 " pdb=" N2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1522 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.134 9.50e-02 1.11e+02 7.44e-02 2.64e+01 pdb=" NE ARG C 147 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.108 9.50e-02 1.11e+02 6.22e-02 2.04e+01 pdb=" NE ARG A 278 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 88 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C HIS C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N THR C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1749 2.76 - 3.30: 9944 3.30 - 3.83: 16237 3.83 - 4.37: 19160 4.37 - 4.90: 33637 Nonbonded interactions: 80727 Sorted by model distance: nonbonded pdb=" OD2 ASP A 507 " pdb=" OG SER C 350 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASN C 111 " pdb=" NH1 ARG C 177 " model vdw 2.288 3.120 nonbonded pdb=" NZ LYS A 246 " pdb=" OE1 GLN A 639 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU A 511 " pdb=" N THR C 351 " model vdw 2.300 3.120 ... (remaining 80722 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 : 0.010 0.066 10365 Z= 0.408 Angle : 0.981 13.060 13998 Z= 0.567 Chirality : 0.063 0.389 1525 Planarity : 0.008 0.108 1792 Dihedral : 17.984 179.608 3904 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.06 (0.20), residues: 1237 helix: -0.99 (0.17), residues: 605 sheet: -0.26 (0.37), residues: 161 loop : -0.14 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 86 HIS 0.014 0.003 HIS A 260 PHE 0.031 0.003 PHE A 586 TYR 0.036 0.007 TYR A 439 ARG 0.085 0.010 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.15701 ( 527) hydrogen bonds : angle 6.82009 ( 1491) covalent geometry : bond 0.00964 (10365) covalent geometry : angle 0.98058 (13998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 ASP cc_start: 0.7468 (t70) cc_final: 0.6992 (t0) REVERT: C 43 VAL cc_start: 0.9134 (t) cc_final: 0.8692 (p) REVERT: B 32 CYS cc_start: 0.6356 (m) cc_final: 0.5938 (m) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2693 time to fit residues: 53.4748 Evaluate side-chains 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 264 GLN A 398 ASN A 406 HIS A 410 ASN A 497 ASN A 638 HIS A 657 HIS C 137 GLN C 246 GLN B 75 GLN B 147 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068768 restraints weight = 21004.591| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.13 r_work: 0.2892 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10365 Z= 0.143 Angle : 0.632 8.035 13998 Z= 0.327 Chirality : 0.044 0.356 1525 Planarity : 0.004 0.058 1792 Dihedral : 17.814 168.404 1426 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.74 % Allowed : 5.45 % Favored : 93.81 % 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: 1.23 (0.23), residues: 1237 helix: 1.26 (0.20), residues: 622 sheet: 0.52 (0.41), residues: 153 loop : 0.51 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.008 0.001 HIS C 275 PHE 0.019 0.001 PHE C 255 TYR 0.018 0.001 TYR A 758 ARG 0.007 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 527) hydrogen bonds : angle 4.65210 ( 1491) covalent geometry : bond 0.00323 (10365) covalent geometry : angle 0.63221 (13998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8719 (m-80) cc_final: 0.8423 (m-80) REVERT: A 177 MET cc_start: 0.8664 (mtt) cc_final: 0.8406 (mtt) REVERT: A 503 MET cc_start: 0.8406 (mtm) cc_final: 0.8202 (mtm) REVERT: A 507 ASP cc_start: 0.8462 (t70) cc_final: 0.7561 (t0) REVERT: A 555 ASP cc_start: 0.7991 (t0) cc_final: 0.7714 (t0) REVERT: C 123 MET cc_start: 0.8967 (mmm) cc_final: 0.8254 (mmm) REVERT: C 157 ASP cc_start: 0.8058 (m-30) cc_final: 0.7740 (m-30) REVERT: C 205 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: B 36 MET cc_start: 0.8908 (mtt) cc_final: 0.8608 (mmm) REVERT: B 105 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7301 (tpp) outliers start: 8 outliers final: 2 residues processed: 113 average time/residue: 0.2634 time to fit residues: 47.1153 Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 140 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 7.9990 chunk 52 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.102949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.070527 restraints weight = 21603.306| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.18 r_work: 0.2885 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10365 Z= 0.135 Angle : 0.558 7.619 13998 Z= 0.286 Chirality : 0.042 0.282 1525 Planarity : 0.004 0.042 1792 Dihedral : 16.839 169.179 1426 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.02 % Allowed : 6.56 % Favored : 92.42 % 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: 1.87 (0.24), residues: 1237 helix: 1.90 (0.21), residues: 613 sheet: 0.74 (0.40), residues: 161 loop : 0.68 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.016 0.001 PHE C 255 TYR 0.014 0.001 TYR A 758 ARG 0.004 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 527) hydrogen bonds : angle 4.27783 ( 1491) covalent geometry : bond 0.00308 (10365) covalent geometry : angle 0.55798 (13998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8711 (m-80) cc_final: 0.8372 (m-80) REVERT: A 177 MET cc_start: 0.8772 (mtt) cc_final: 0.8507 (mtt) REVERT: A 305 MET cc_start: 0.8790 (tpp) cc_final: 0.8275 (tpp) REVERT: A 503 MET cc_start: 0.8345 (mtm) cc_final: 0.7957 (mmm) REVERT: A 507 ASP cc_start: 0.8479 (t70) cc_final: 0.7529 (t0) REVERT: C 14 SER cc_start: 0.8646 (p) cc_final: 0.8240 (p) REVERT: C 123 MET cc_start: 0.8957 (mmm) cc_final: 0.8311 (mmm) REVERT: C 137 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: C 157 ASP cc_start: 0.8009 (m-30) cc_final: 0.7581 (m-30) REVERT: B 93 PHE cc_start: 0.8408 (m-80) cc_final: 0.7880 (m-80) REVERT: B 105 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7240 (tpp) outliers start: 11 outliers final: 4 residues processed: 90 average time/residue: 0.1868 time to fit residues: 26.4449 Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 0.1980 chunk 121 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN C 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067759 restraints weight = 21296.818| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.20 r_work: 0.2865 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10365 Z= 0.152 Angle : 0.558 8.793 13998 Z= 0.280 Chirality : 0.042 0.372 1525 Planarity : 0.004 0.041 1792 Dihedral : 15.751 170.850 1426 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.20 % Allowed : 6.93 % Favored : 91.87 % 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: 2.01 (0.24), residues: 1237 helix: 2.04 (0.21), residues: 619 sheet: 0.71 (0.40), residues: 161 loop : 0.74 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.010 0.001 HIS B 147 PHE 0.014 0.001 PHE A 553 TYR 0.012 0.001 TYR A 259 ARG 0.007 0.000 ARG A 779 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 527) hydrogen bonds : angle 4.14173 ( 1491) covalent geometry : bond 0.00348 (10365) covalent geometry : angle 0.55817 (13998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8770 (m-80) cc_final: 0.8424 (m-80) REVERT: A 364 MET cc_start: 0.9128 (mmt) cc_final: 0.8714 (mmt) REVERT: A 503 MET cc_start: 0.8448 (mtm) cc_final: 0.8048 (mmm) REVERT: A 507 ASP cc_start: 0.8529 (t70) cc_final: 0.7565 (t0) REVERT: A 575 GLU cc_start: 0.8447 (mp0) cc_final: 0.8140 (mm-30) REVERT: C 14 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8192 (p) REVERT: C 137 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: C 157 ASP cc_start: 0.7974 (m-30) cc_final: 0.7421 (m-30) REVERT: C 167 GLU cc_start: 0.8494 (mp0) cc_final: 0.8261 (mp0) REVERT: C 205 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: B 93 PHE cc_start: 0.8389 (m-80) cc_final: 0.7931 (m-80) REVERT: B 105 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7323 (tpp) outliers start: 13 outliers final: 5 residues processed: 92 average time/residue: 0.2648 time to fit residues: 36.6601 Evaluate side-chains 87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.100704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068105 restraints weight = 21308.886| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.20 r_work: 0.2877 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10365 Z= 0.131 Angle : 0.531 8.885 13998 Z= 0.265 Chirality : 0.041 0.331 1525 Planarity : 0.003 0.040 1792 Dihedral : 15.450 171.394 1426 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.76 % Allowed : 7.21 % Favored : 91.04 % 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: 2.11 (0.24), residues: 1237 helix: 2.17 (0.21), residues: 619 sheet: 0.70 (0.40), residues: 161 loop : 0.73 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.007 0.001 HIS B 147 PHE 0.013 0.001 PHE C 255 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 527) hydrogen bonds : angle 4.01637 ( 1491) covalent geometry : bond 0.00300 (10365) covalent geometry : angle 0.53142 (13998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8756 (m-80) cc_final: 0.8393 (m-80) REVERT: A 39 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: A 305 MET cc_start: 0.8754 (tpp) cc_final: 0.8194 (tpp) REVERT: A 503 MET cc_start: 0.8419 (mtm) cc_final: 0.8048 (mmm) REVERT: A 507 ASP cc_start: 0.8544 (t70) cc_final: 0.7538 (t0) REVERT: A 575 GLU cc_start: 0.8513 (mp0) cc_final: 0.8297 (mm-30) REVERT: C 14 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8302 (p) REVERT: C 137 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: C 205 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: C 316 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: B 93 PHE cc_start: 0.8402 (m-80) cc_final: 0.7946 (m-80) REVERT: B 105 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7326 (tpp) outliers start: 19 outliers final: 7 residues processed: 94 average time/residue: 0.2179 time to fit residues: 31.4850 Evaluate side-chains 89 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067230 restraints weight = 21427.528| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.21 r_work: 0.2857 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10365 Z= 0.157 Angle : 0.539 8.026 13998 Z= 0.268 Chirality : 0.042 0.338 1525 Planarity : 0.004 0.042 1792 Dihedral : 15.601 173.279 1426 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.76 % Allowed : 8.60 % Favored : 89.65 % 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: 2.06 (0.24), residues: 1237 helix: 2.17 (0.21), residues: 615 sheet: 0.63 (0.40), residues: 162 loop : 0.67 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.013 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.013 0.001 TYR A 259 ARG 0.003 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 527) hydrogen bonds : angle 3.99835 ( 1491) covalent geometry : bond 0.00364 (10365) covalent geometry : angle 0.53948 (13998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8728 (m-80) cc_final: 0.8361 (m-80) REVERT: A 39 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: A 132 MET cc_start: 0.7778 (ttm) cc_final: 0.7052 (tpp) REVERT: A 503 MET cc_start: 0.8504 (mtm) cc_final: 0.8138 (mmm) REVERT: A 507 ASP cc_start: 0.8569 (t70) cc_final: 0.7554 (t0) REVERT: C 14 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8224 (p) REVERT: C 137 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: C 157 ASP cc_start: 0.7991 (m-30) cc_final: 0.7408 (m-30) REVERT: C 176 MET cc_start: 0.9125 (tpp) cc_final: 0.8898 (mmm) REVERT: C 205 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: C 316 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: B 73 MET cc_start: 0.5738 (mmm) cc_final: 0.4749 (ptt) REVERT: B 93 PHE cc_start: 0.8385 (m-80) cc_final: 0.7994 (m-80) REVERT: B 105 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7336 (tpp) REVERT: B 119 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7740 (tppt) outliers start: 19 outliers final: 9 residues processed: 90 average time/residue: 0.1918 time to fit residues: 27.0849 Evaluate side-chains 88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 121 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.099968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.067327 restraints weight = 21515.073| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.20 r_work: 0.2857 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10365 Z= 0.145 Angle : 0.529 7.406 13998 Z= 0.263 Chirality : 0.041 0.325 1525 Planarity : 0.004 0.044 1792 Dihedral : 15.916 177.638 1426 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.66 % Allowed : 9.24 % Favored : 89.09 % 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: 2.04 (0.24), residues: 1237 helix: 2.21 (0.21), residues: 614 sheet: 0.53 (0.39), residues: 162 loop : 0.61 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 79 HIS 0.011 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.012 0.001 TYR A 259 ARG 0.003 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 527) hydrogen bonds : angle 3.94412 ( 1491) covalent geometry : bond 0.00336 (10365) covalent geometry : angle 0.52878 (13998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8732 (m-80) cc_final: 0.8354 (m-80) REVERT: A 39 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: A 62 LEU cc_start: 0.8829 (tp) cc_final: 0.8554 (tp) REVERT: A 132 MET cc_start: 0.7822 (ttm) cc_final: 0.7165 (tpp) REVERT: A 305 MET cc_start: 0.8830 (tpp) cc_final: 0.8251 (tpp) REVERT: A 503 MET cc_start: 0.8498 (mtm) cc_final: 0.8148 (mmm) REVERT: A 507 ASP cc_start: 0.8598 (t70) cc_final: 0.7592 (t0) REVERT: A 553 PHE cc_start: 0.8322 (t80) cc_final: 0.7853 (t80) REVERT: C 137 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: C 176 MET cc_start: 0.9119 (tpp) cc_final: 0.8867 (mmm) REVERT: C 205 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: C 316 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: B 73 MET cc_start: 0.5647 (mmm) cc_final: 0.4714 (ptt) REVERT: B 93 PHE cc_start: 0.8407 (m-80) cc_final: 0.8032 (m-80) REVERT: B 105 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7344 (tpp) REVERT: B 119 LYS cc_start: 0.8460 (mmtm) cc_final: 0.7930 (tppt) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.2677 time to fit residues: 40.0465 Evaluate side-chains 93 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 84 optimal weight: 0.0470 chunk 61 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.101273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068837 restraints weight = 21442.696| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.21 r_work: 0.2882 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10365 Z= 0.108 Angle : 0.516 8.220 13998 Z= 0.255 Chirality : 0.040 0.298 1525 Planarity : 0.003 0.041 1792 Dihedral : 16.070 178.631 1426 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.11 % Allowed : 10.54 % Favored : 88.35 % 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: 2.12 (0.24), residues: 1237 helix: 2.33 (0.21), residues: 614 sheet: 0.45 (0.39), residues: 162 loop : 0.62 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.009 0.001 HIS B 147 PHE 0.013 0.001 PHE C 255 TYR 0.009 0.001 TYR A 456 ARG 0.003 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 527) hydrogen bonds : angle 3.84866 ( 1491) covalent geometry : bond 0.00244 (10365) covalent geometry : angle 0.51615 (13998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8748 (m-80) cc_final: 0.8365 (m-80) REVERT: A 62 LEU cc_start: 0.8803 (tp) cc_final: 0.8524 (tp) REVERT: A 132 MET cc_start: 0.7869 (ttm) cc_final: 0.7207 (tpp) REVERT: A 305 MET cc_start: 0.8801 (tpp) cc_final: 0.8248 (tpp) REVERT: A 503 MET cc_start: 0.8434 (mtm) cc_final: 0.8124 (mmm) REVERT: A 507 ASP cc_start: 0.8594 (t70) cc_final: 0.7588 (t0) REVERT: C 123 MET cc_start: 0.8916 (mmm) cc_final: 0.8465 (mmm) REVERT: C 137 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: C 176 MET cc_start: 0.9142 (tpp) cc_final: 0.8912 (mmm) REVERT: C 205 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: B 73 MET cc_start: 0.5698 (mmm) cc_final: 0.4867 (ptt) REVERT: B 93 PHE cc_start: 0.8359 (m-80) cc_final: 0.7985 (m-80) REVERT: B 119 LYS cc_start: 0.8466 (mmtm) cc_final: 0.7931 (tppt) outliers start: 12 outliers final: 9 residues processed: 93 average time/residue: 0.2382 time to fit residues: 34.5334 Evaluate side-chains 88 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 36 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 99 optimal weight: 0.0970 chunk 114 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.101193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068660 restraints weight = 21459.220| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.21 r_work: 0.2882 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10365 Z= 0.115 Angle : 0.535 8.600 13998 Z= 0.261 Chirality : 0.040 0.289 1525 Planarity : 0.003 0.038 1792 Dihedral : 16.095 179.123 1426 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.29 % Allowed : 10.63 % Favored : 88.08 % 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: 2.17 (0.24), residues: 1237 helix: 2.40 (0.21), residues: 608 sheet: 0.40 (0.39), residues: 162 loop : 0.65 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.009 0.001 HIS B 147 PHE 0.020 0.001 PHE A 553 TYR 0.010 0.001 TYR A 259 ARG 0.002 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 527) hydrogen bonds : angle 3.83542 ( 1491) covalent geometry : bond 0.00264 (10365) covalent geometry : angle 0.53476 (13998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8762 (m-80) cc_final: 0.8373 (m-80) REVERT: A 132 MET cc_start: 0.7873 (ttm) cc_final: 0.7185 (tpp) REVERT: A 305 MET cc_start: 0.8815 (tpp) cc_final: 0.8270 (tpp) REVERT: A 503 MET cc_start: 0.8435 (mtm) cc_final: 0.8118 (mmm) REVERT: A 507 ASP cc_start: 0.8589 (t70) cc_final: 0.7567 (t0) REVERT: C 123 MET cc_start: 0.8910 (mmm) cc_final: 0.8450 (mmm) REVERT: C 137 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: C 176 MET cc_start: 0.9137 (tpp) cc_final: 0.8891 (mmm) REVERT: C 205 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: C 316 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: C 325 MET cc_start: 0.8971 (tpt) cc_final: 0.8757 (tpt) REVERT: B 73 MET cc_start: 0.5822 (mmm) cc_final: 0.4946 (ptt) REVERT: B 93 PHE cc_start: 0.8349 (m-80) cc_final: 0.7977 (m-80) REVERT: B 119 LYS cc_start: 0.8460 (mmtm) cc_final: 0.7833 (tppt) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 0.1931 time to fit residues: 27.6724 Evaluate side-chains 87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 36 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 84 optimal weight: 0.0470 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 78 optimal weight: 0.3980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.101316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068764 restraints weight = 21332.619| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.23 r_work: 0.2883 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.117 Angle : 0.547 8.891 13998 Z= 0.265 Chirality : 0.041 0.281 1525 Planarity : 0.003 0.038 1792 Dihedral : 16.114 179.717 1426 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.29 % Allowed : 10.81 % Favored : 87.89 % 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: 2.11 (0.24), residues: 1237 helix: 2.34 (0.21), residues: 614 sheet: 0.43 (0.40), residues: 162 loop : 0.58 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 79 HIS 0.013 0.001 HIS B 147 PHE 0.015 0.001 PHE A 553 TYR 0.010 0.001 TYR A 259 ARG 0.002 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 527) hydrogen bonds : angle 3.85089 ( 1491) covalent geometry : bond 0.00268 (10365) covalent geometry : angle 0.54669 (13998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8730 (m-80) cc_final: 0.8333 (m-80) REVERT: A 132 MET cc_start: 0.7917 (ttm) cc_final: 0.7343 (tpp) REVERT: A 305 MET cc_start: 0.8814 (tpp) cc_final: 0.8268 (tpp) REVERT: A 364 MET cc_start: 0.9179 (mmm) cc_final: 0.8788 (mpp) REVERT: A 503 MET cc_start: 0.8407 (mtm) cc_final: 0.8119 (mmm) REVERT: A 507 ASP cc_start: 0.8596 (t70) cc_final: 0.7571 (t0) REVERT: A 715 MET cc_start: 0.8596 (ptt) cc_final: 0.8320 (ptt) REVERT: C 123 MET cc_start: 0.8912 (mmm) cc_final: 0.8469 (mmm) REVERT: C 137 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: C 176 MET cc_start: 0.9141 (tpp) cc_final: 0.8899 (mmm) REVERT: C 205 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: C 316 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: C 325 MET cc_start: 0.9014 (tpt) cc_final: 0.8672 (tpt) REVERT: B 73 MET cc_start: 0.5864 (mmm) cc_final: 0.5025 (ptt) REVERT: B 93 PHE cc_start: 0.8384 (m-80) cc_final: 0.8117 (m-80) REVERT: B 119 LYS cc_start: 0.8429 (mmtm) cc_final: 0.7810 (tppt) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 0.1842 time to fit residues: 26.4374 Evaluate side-chains 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 36 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.101012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.068478 restraints weight = 21199.916| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.20 r_work: 0.2880 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10365 Z= 0.122 Angle : 0.559 15.842 13998 Z= 0.269 Chirality : 0.040 0.277 1525 Planarity : 0.003 0.037 1792 Dihedral : 16.121 179.749 1426 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.11 % Allowed : 10.91 % Favored : 87.99 % 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: 2.13 (0.24), residues: 1237 helix: 2.35 (0.21), residues: 614 sheet: 0.47 (0.40), residues: 162 loop : 0.60 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 79 HIS 0.013 0.001 HIS B 147 PHE 0.016 0.001 PHE B 93 TYR 0.010 0.001 TYR A 259 ARG 0.003 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 527) hydrogen bonds : angle 3.84383 ( 1491) covalent geometry : bond 0.00282 (10365) covalent geometry : angle 0.55919 (13998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5820.22 seconds wall clock time: 105 minutes 35.29 seconds (6335.29 seconds total)