Starting phenix.real_space_refine on Sat Dec 28 11:05:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uxa_26856/12_2024/7uxa_26856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uxa_26856/12_2024/7uxa_26856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uxa_26856/12_2024/7uxa_26856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uxa_26856/12_2024/7uxa_26856.map" model { file = "/net/cci-nas-00/data/ceres_data/7uxa_26856/12_2024/7uxa_26856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uxa_26856/12_2024/7uxa_26856.cif" } resolution = 3.28 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= 0.052 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 P 77 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 4890 2.51 5 N 1420 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1762 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 117} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1615 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2105 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1665 Inner-chain residues flagged as termini: ['pdbres=" A E 47 "'] Classifications: {'RNA': 78} Modifications used: {'5*END': 1, 'p5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.24, per 1000 atoms: 0.77 Number of scatterers: 8120 At special positions: 0 Unit cell: (87.608, 86.676, 123.024, 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) S 26 16.00 P 77 15.00 Mg 2 11.99 O 1705 8.00 N 1420 7.00 C 4890 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: 2.52 Conformation dependent library (CDL) restraints added in 859.3 milliseconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 35.4% alpha, 16.3% beta 27 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 83 through 101 removed outlier: 3.593A pdb=" N GLN A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.608A pdb=" N ASP A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'B' and resid 44 through 53 removed outlier: 4.314A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 53 " --> pdb=" O MET B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 73 Processing helix chain 'B' and resid 116 through 131 Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 430 through 443 removed outlier: 3.824A pdb=" N GLU C 435 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Proline residue: C 437 - end of helix removed outlier: 3.622A pdb=" N ILE C 443 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 27 removed outlier: 3.851A pdb=" N ARG D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 67 removed outlier: 3.707A pdb=" N ALA D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.611A pdb=" N THR D 101 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.673A pdb=" N LEU D 145 " --> pdb=" O TYR D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.842A pdb=" N ALA D 459 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.512A pdb=" N SER A 11 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 2 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 69 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL A 4 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.524A pdb=" N GLU D 72 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG D 70 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 235 removed outlier: 4.610A pdb=" N LEU A 289 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 291 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 235 removed outlier: 4.610A pdb=" N LEU A 289 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 291 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 288 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 302 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 104 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA B 142 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 106 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL B 144 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 108 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE B 90 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 269 removed outlier: 4.115A pdb=" N LEU B 114 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 297 through 299 removed outlier: 3.850A pdb=" N VAL C 49 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE C 40 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR C 317 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA C 42 " --> pdb=" O TYR C 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.025A pdb=" N TYR C 380 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 387 removed outlier: 3.540A pdb=" N LEU C 423 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU C 447 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS D 474 " --> pdb=" O ALA D 503 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL D 505 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER D 476 " --> pdb=" O VAL D 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 104 through 106 264 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2137 1.33 - 1.45: 1945 1.45 - 1.57: 4193 1.57 - 1.69: 153 1.69 - 1.81: 41 Bond restraints: 8469 Sorted by residual: bond pdb=" CA GLY B 94 " pdb=" C GLY B 94 " ideal model delta sigma weight residual 1.521 1.511 0.011 1.13e-02 7.83e+03 8.78e-01 bond pdb=" CB TRP D 99 " pdb=" CG TRP D 99 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.02e-01 bond pdb=" CA ALA A 286 " pdb=" C ALA A 286 " ideal model delta sigma weight residual 1.522 1.531 -0.009 1.08e-02 8.57e+03 6.87e-01 bond pdb=" CA ALA C 377 " pdb=" C ALA C 377 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.49e-01 bond pdb=" CA GLU C 458 " pdb=" C GLU C 458 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.10e-02 8.26e+03 6.09e-01 ... (remaining 8464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 11286 1.19 - 2.38: 463 2.38 - 3.57: 105 3.57 - 4.76: 13 4.76 - 5.95: 2 Bond angle restraints: 11869 Sorted by residual: angle pdb=" N ASP A 243 " pdb=" CA ASP A 243 " pdb=" C ASP A 243 " ideal model delta sigma weight residual 114.75 111.06 3.69 1.26e+00 6.30e-01 8.60e+00 angle pdb=" N THR D 429 " pdb=" CA THR D 429 " pdb=" C THR D 429 " ideal model delta sigma weight residual 107.23 111.62 -4.39 1.67e+00 3.59e-01 6.92e+00 angle pdb=" N LYS C 371 " pdb=" CA LYS C 371 " pdb=" C LYS C 371 " ideal model delta sigma weight residual 108.19 111.38 -3.19 1.29e+00 6.01e-01 6.13e+00 angle pdb=" N TYR C 362 " pdb=" CA TYR C 362 " pdb=" C TYR C 362 " ideal model delta sigma weight residual 109.65 105.95 3.70 1.56e+00 4.11e-01 5.64e+00 angle pdb=" N VAL C 335 " pdb=" CA VAL C 335 " pdb=" C VAL C 335 " ideal model delta sigma weight residual 113.07 110.04 3.03 1.36e+00 5.41e-01 4.97e+00 ... (remaining 11864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 4821 24.49 - 48.98: 204 48.98 - 73.47: 139 73.47 - 97.97: 11 97.97 - 122.46: 3 Dihedral angle restraints: 5178 sinusoidal: 2805 harmonic: 2373 Sorted by residual: dihedral pdb=" CA LEU C 360 " pdb=" C LEU C 360 " pdb=" N LYS C 361 " pdb=" CA LYS C 361 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" O4' G E 72 " pdb=" C1' G E 72 " pdb=" N9 G E 72 " pdb=" C4 G E 72 " ideal model delta sinusoidal sigma weight residual -90.00 -19.43 -70.57 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" O4' A E 52 " pdb=" C1' A E 52 " pdb=" N9 A E 52 " pdb=" C4 A E 52 " ideal model delta sinusoidal sigma weight residual -106.00 -158.89 52.89 1 1.70e+01 3.46e-03 1.32e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1053 0.037 - 0.074: 249 0.074 - 0.111: 69 0.111 - 0.147: 12 0.147 - 0.184: 1 Chirality restraints: 1384 Sorted by residual: chirality pdb=" C1' A E 74 " pdb=" O4' A E 74 " pdb=" C2' A E 74 " pdb=" N9 A E 74 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" C1' G E 22 " pdb=" O4' G E 22 " pdb=" C2' G E 22 " pdb=" N9 G E 22 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1381 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 373 " -0.036 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO C 374 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 374 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 374 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A E 74 " 0.024 2.00e-02 2.50e+03 1.10e-02 3.32e+00 pdb=" N9 A E 74 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A E 74 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A E 74 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A E 74 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A E 74 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A E 74 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A E 74 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A E 74 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A E 74 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A E 74 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 6 " -0.020 2.00e-02 2.50e+03 1.08e-02 2.61e+00 pdb=" N1 U E 6 " 0.024 2.00e-02 2.50e+03 pdb=" C2 U E 6 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U E 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U E 6 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U E 6 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U E 6 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U E 6 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U E 6 " 0.003 2.00e-02 2.50e+03 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 142 2.65 - 3.21: 7217 3.21 - 3.77: 13257 3.77 - 4.34: 17916 4.34 - 4.90: 28118 Nonbonded interactions: 66650 Sorted by model distance: nonbonded pdb=" OP1 G E 9 " pdb="MG MG E 101 " model vdw 2.084 2.170 nonbonded pdb=" OG SER D 495 " pdb=" O VAL D 498 " model vdw 2.168 3.040 nonbonded pdb=" OE1 GLU A 62 " pdb=" OH TYR A 221 " model vdw 2.199 3.040 nonbonded pdb=" NH2 ARG D 27 " pdb=" OP1 G E 17 " model vdw 2.252 3.120 nonbonded pdb=" OE1 GLU D 122 " pdb=" OH TYR D 155 " model vdw 2.255 3.040 ... (remaining 66645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.028 8469 Z= 0.221 Angle : 0.577 5.955 11869 Z= 0.330 Chirality : 0.036 0.184 1384 Planarity : 0.004 0.054 1229 Dihedral : 16.774 122.458 3648 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.88 % Allowed : 6.00 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.97 (0.31), residues: 805 helix: 0.29 (0.31), residues: 276 sheet: -1.95 (0.45), residues: 128 loop : -0.75 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.003 0.001 HIS A 211 PHE 0.013 0.001 PHE A 244 TYR 0.010 0.001 TYR D 155 ARG 0.003 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.7116 (mtp180) REVERT: B 59 GLN cc_start: 0.8097 (mt0) cc_final: 0.7868 (mp10) REVERT: B 81 CYS cc_start: 0.9034 (m) cc_final: 0.8592 (p) REVERT: B 147 ASP cc_start: 0.8943 (t0) cc_final: 0.8663 (t0) REVERT: B 161 LEU cc_start: 0.8177 (mt) cc_final: 0.7880 (pt) REVERT: C 46 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7287 (m-40) REVERT: C 58 GLU cc_start: 0.5999 (mt-10) cc_final: 0.4964 (tp30) REVERT: C 317 TYR cc_start: 0.6729 (m-80) cc_final: 0.6519 (m-80) REVERT: C 367 LEU cc_start: 0.8298 (mt) cc_final: 0.7883 (mp) REVERT: C 429 MET cc_start: 0.6062 (tmm) cc_final: 0.5803 (tmm) outliers start: 6 outliers final: 1 residues processed: 161 average time/residue: 0.2321 time to fit residues: 49.8656 Evaluate side-chains 106 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 447 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN C 46 ASN C 47 ASN C 413 ASN D 35 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 522 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8469 Z= 0.199 Angle : 0.529 5.597 11869 Z= 0.271 Chirality : 0.038 0.164 1384 Planarity : 0.004 0.050 1229 Dihedral : 18.918 116.124 2121 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.61 % Allowed : 11.27 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.48 (0.31), residues: 805 helix: 0.72 (0.32), residues: 272 sheet: -1.58 (0.45), residues: 134 loop : -0.48 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.003 0.001 HIS B 116 PHE 0.012 0.001 PHE C 305 TYR 0.016 0.001 TYR B 67 ARG 0.007 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7548 (mmt-90) cc_final: 0.7073 (mtp180) REVERT: B 161 LEU cc_start: 0.8131 (mt) cc_final: 0.7825 (pt) REVERT: C 44 MET cc_start: 0.8160 (tpp) cc_final: 0.7725 (tpt) REVERT: C 58 GLU cc_start: 0.5976 (mt-10) cc_final: 0.5064 (tp30) REVERT: C 348 TYR cc_start: 0.7288 (t80) cc_final: 0.6940 (t80) REVERT: C 367 LEU cc_start: 0.8168 (mt) cc_final: 0.7786 (mp) REVERT: C 413 ASN cc_start: 0.8019 (m-40) cc_final: 0.7791 (m110) REVERT: C 429 MET cc_start: 0.6147 (tmm) cc_final: 0.5909 (tmm) REVERT: D 73 ARG cc_start: 0.7491 (pmt170) cc_final: 0.7261 (ptt-90) REVERT: D 90 GLU cc_start: 0.8425 (tt0) cc_final: 0.8116 (pt0) REVERT: D 460 THR cc_start: 0.9299 (p) cc_final: 0.8897 (t) REVERT: D 465 ASN cc_start: 0.8398 (p0) cc_final: 0.8119 (p0) REVERT: D 509 ASP cc_start: 0.8578 (t0) cc_final: 0.8307 (t70) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 0.2438 time to fit residues: 39.6000 Evaluate side-chains 109 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 519 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8469 Z= 0.180 Angle : 0.514 5.580 11869 Z= 0.263 Chirality : 0.037 0.168 1384 Planarity : 0.004 0.050 1229 Dihedral : 18.779 114.373 2116 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.46 % Allowed : 13.03 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.28 (0.31), residues: 805 helix: 0.85 (0.31), residues: 272 sheet: -1.33 (0.45), residues: 134 loop : -0.39 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 63 HIS 0.002 0.001 HIS B 116 PHE 0.011 0.001 PHE A 233 TYR 0.015 0.001 TYR B 67 ARG 0.008 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7123 (mtp180) REVERT: B 59 GLN cc_start: 0.8147 (mp10) cc_final: 0.7929 (mp10) REVERT: B 161 LEU cc_start: 0.8125 (mt) cc_final: 0.7813 (pt) REVERT: C 44 MET cc_start: 0.8075 (tpp) cc_final: 0.7797 (tpt) REVERT: C 348 TYR cc_start: 0.7334 (t80) cc_final: 0.6873 (t80) REVERT: C 413 ASN cc_start: 0.7964 (m-40) cc_final: 0.7736 (m110) REVERT: C 419 MET cc_start: 0.7873 (mtt) cc_final: 0.7544 (mtt) REVERT: C 429 MET cc_start: 0.6006 (tmm) cc_final: 0.5792 (tmm) REVERT: D 63 TRP cc_start: 0.8710 (m100) cc_final: 0.8354 (m100) REVERT: D 73 ARG cc_start: 0.7432 (pmt170) cc_final: 0.7207 (ptt-90) REVERT: D 90 GLU cc_start: 0.8431 (tt0) cc_final: 0.8096 (pm20) REVERT: D 460 THR cc_start: 0.9281 (p) cc_final: 0.8895 (t) REVERT: D 465 ASN cc_start: 0.8502 (p0) cc_final: 0.8228 (p0) outliers start: 10 outliers final: 3 residues processed: 118 average time/residue: 0.2184 time to fit residues: 34.5782 Evaluate side-chains 99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 43 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN D 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8469 Z= 0.186 Angle : 0.506 5.810 11869 Z= 0.259 Chirality : 0.037 0.169 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.693 111.853 2116 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.61 % Allowed : 13.03 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.31), residues: 805 helix: 1.02 (0.31), residues: 272 sheet: -1.20 (0.46), residues: 134 loop : -0.32 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 354 HIS 0.002 0.000 HIS B 116 PHE 0.014 0.001 PHE A 233 TYR 0.013 0.001 TYR D 470 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7561 (mmt-90) cc_final: 0.7157 (mtp180) REVERT: A 205 GLN cc_start: 0.6571 (tm-30) cc_final: 0.6088 (tm-30) REVERT: B 59 GLN cc_start: 0.8203 (mp10) cc_final: 0.7865 (mp10) REVERT: B 64 PHE cc_start: 0.8565 (t80) cc_final: 0.8298 (t80) REVERT: B 161 LEU cc_start: 0.8165 (mt) cc_final: 0.7816 (pt) REVERT: C 44 MET cc_start: 0.8006 (tpp) cc_final: 0.7588 (tpt) REVERT: C 348 TYR cc_start: 0.7484 (t80) cc_final: 0.6932 (t80) REVERT: C 413 ASN cc_start: 0.7948 (m-40) cc_final: 0.7702 (m110) REVERT: C 419 MET cc_start: 0.7866 (mtt) cc_final: 0.7616 (ttm) REVERT: D 63 TRP cc_start: 0.8651 (m100) cc_final: 0.8318 (m100) REVERT: D 73 ARG cc_start: 0.7448 (pmt170) cc_final: 0.7246 (ptt-90) REVERT: D 90 GLU cc_start: 0.8429 (tt0) cc_final: 0.8075 (pm20) REVERT: D 460 THR cc_start: 0.9255 (p) cc_final: 0.8892 (t) REVERT: D 465 ASN cc_start: 0.8563 (p0) cc_final: 0.8243 (p0) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.2264 time to fit residues: 33.8330 Evaluate side-chains 102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 519 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 72 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8469 Z= 0.155 Angle : 0.484 5.861 11869 Z= 0.248 Chirality : 0.036 0.171 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.646 110.411 2116 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.46 % Allowed : 14.64 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.08 (0.31), residues: 805 helix: 1.16 (0.32), residues: 274 sheet: -1.01 (0.46), residues: 132 loop : -0.25 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 354 HIS 0.002 0.000 HIS B 77 PHE 0.012 0.001 PHE A 233 TYR 0.010 0.001 TYR B 67 ARG 0.005 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.7204 (mtp180) REVERT: A 94 PHE cc_start: 0.8059 (t80) cc_final: 0.7729 (t80) REVERT: A 205 GLN cc_start: 0.6626 (tm-30) cc_final: 0.6131 (tm-30) REVERT: B 40 MET cc_start: 0.6401 (mtp) cc_final: 0.5895 (mtp) REVERT: B 59 GLN cc_start: 0.8198 (mp10) cc_final: 0.7784 (mp10) REVERT: B 124 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8392 (mmtp) REVERT: B 132 ASP cc_start: 0.8127 (t70) cc_final: 0.7887 (t0) REVERT: B 152 TYR cc_start: 0.8052 (m-80) cc_final: 0.7725 (m-80) REVERT: B 161 LEU cc_start: 0.8156 (mt) cc_final: 0.7838 (pt) REVERT: C 44 MET cc_start: 0.7945 (tpp) cc_final: 0.7468 (tpt) REVERT: C 348 TYR cc_start: 0.7605 (t80) cc_final: 0.7002 (t80) REVERT: C 413 ASN cc_start: 0.7966 (m-40) cc_final: 0.7700 (m110) REVERT: C 419 MET cc_start: 0.7769 (mtt) cc_final: 0.7498 (ttm) REVERT: D 63 TRP cc_start: 0.8642 (m100) cc_final: 0.8262 (m100) REVERT: D 90 GLU cc_start: 0.8375 (tt0) cc_final: 0.8046 (pm20) REVERT: D 460 THR cc_start: 0.9163 (p) cc_final: 0.8834 (t) REVERT: D 465 ASN cc_start: 0.8577 (p0) cc_final: 0.8262 (p0) outliers start: 10 outliers final: 5 residues processed: 112 average time/residue: 0.2026 time to fit residues: 31.5979 Evaluate side-chains 98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 78 HIS ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8469 Z= 0.166 Angle : 0.481 5.815 11869 Z= 0.244 Chirality : 0.036 0.173 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.619 111.411 2116 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.76 % Allowed : 15.08 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.16 (0.31), residues: 805 helix: 1.21 (0.31), residues: 274 sheet: -0.86 (0.46), residues: 130 loop : -0.24 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 354 HIS 0.001 0.000 HIS B 116 PHE 0.013 0.001 PHE B 64 TYR 0.014 0.001 TYR D 470 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7562 (mmt-90) cc_final: 0.7219 (mtp180) REVERT: A 205 GLN cc_start: 0.6611 (tm-30) cc_final: 0.6115 (tm-30) REVERT: B 40 MET cc_start: 0.6511 (mtp) cc_final: 0.5977 (mtp) REVERT: B 59 GLN cc_start: 0.8224 (mp10) cc_final: 0.7798 (mp10) REVERT: B 124 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8433 (mmtp) REVERT: B 132 ASP cc_start: 0.8043 (t70) cc_final: 0.7781 (t0) REVERT: B 152 TYR cc_start: 0.8022 (m-80) cc_final: 0.7776 (m-80) REVERT: B 161 LEU cc_start: 0.8207 (mt) cc_final: 0.7872 (pt) REVERT: C 44 MET cc_start: 0.7926 (tpp) cc_final: 0.7543 (tpt) REVERT: C 348 TYR cc_start: 0.7736 (t80) cc_final: 0.7150 (t80) REVERT: C 413 ASN cc_start: 0.7970 (m-40) cc_final: 0.7729 (m110) REVERT: C 419 MET cc_start: 0.7767 (mtt) cc_final: 0.7483 (ttm) REVERT: D 90 GLU cc_start: 0.8375 (tt0) cc_final: 0.8063 (pm20) REVERT: D 460 THR cc_start: 0.9161 (p) cc_final: 0.8843 (t) REVERT: D 465 ASN cc_start: 0.8611 (p0) cc_final: 0.8256 (p0) outliers start: 12 outliers final: 6 residues processed: 107 average time/residue: 0.1983 time to fit residues: 29.9477 Evaluate side-chains 97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.0000 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.0070 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8469 Z= 0.139 Angle : 0.481 6.633 11869 Z= 0.242 Chirality : 0.036 0.172 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.587 109.097 2116 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.32 % Allowed : 16.98 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 805 helix: 1.29 (0.32), residues: 274 sheet: -0.69 (0.46), residues: 130 loop : -0.17 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 63 HIS 0.002 0.000 HIS B 116 PHE 0.009 0.001 PHE C 305 TYR 0.012 0.001 TYR D 470 ARG 0.005 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.7189 (mtp-110) REVERT: A 205 GLN cc_start: 0.6590 (tm-30) cc_final: 0.6097 (tm-30) REVERT: B 40 MET cc_start: 0.6551 (mtp) cc_final: 0.5990 (mtp) REVERT: B 59 GLN cc_start: 0.8193 (mp10) cc_final: 0.7773 (mp10) REVERT: B 124 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8426 (mmtp) REVERT: B 132 ASP cc_start: 0.8130 (t70) cc_final: 0.7887 (t0) REVERT: B 152 TYR cc_start: 0.7881 (m-80) cc_final: 0.7310 (m-80) REVERT: B 161 LEU cc_start: 0.8154 (mt) cc_final: 0.7804 (pt) REVERT: C 44 MET cc_start: 0.8033 (tpp) cc_final: 0.7564 (tpt) REVERT: C 348 TYR cc_start: 0.7634 (t80) cc_final: 0.7054 (t80) REVERT: C 413 ASN cc_start: 0.7992 (m-40) cc_final: 0.7758 (m110) REVERT: C 419 MET cc_start: 0.7765 (mtt) cc_final: 0.7516 (ttm) REVERT: D 63 TRP cc_start: 0.8590 (m100) cc_final: 0.8345 (m100) REVERT: D 90 GLU cc_start: 0.8333 (tt0) cc_final: 0.8018 (pm20) REVERT: D 460 THR cc_start: 0.9112 (p) cc_final: 0.8819 (t) REVERT: D 465 ASN cc_start: 0.8603 (p0) cc_final: 0.8242 (p0) outliers start: 9 outliers final: 7 residues processed: 105 average time/residue: 0.1881 time to fit residues: 27.9246 Evaluate side-chains 99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8469 Z= 0.178 Angle : 0.496 5.787 11869 Z= 0.249 Chirality : 0.036 0.171 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.555 108.467 2116 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.32 % Allowed : 16.84 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 805 helix: 1.28 (0.31), residues: 274 sheet: -0.60 (0.46), residues: 130 loop : -0.18 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 63 HIS 0.001 0.000 HIS A 79 PHE 0.014 0.001 PHE B 64 TYR 0.013 0.001 TYR D 155 ARG 0.005 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7459 (mmt-90) cc_final: 0.7213 (mtp-110) REVERT: A 205 GLN cc_start: 0.6661 (tm-30) cc_final: 0.6142 (tm-30) REVERT: B 40 MET cc_start: 0.6526 (mtp) cc_final: 0.5891 (mtp) REVERT: B 59 GLN cc_start: 0.8196 (mp10) cc_final: 0.7760 (mp10) REVERT: B 124 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8453 (mmtp) REVERT: B 132 ASP cc_start: 0.7979 (t70) cc_final: 0.7756 (t0) REVERT: B 152 TYR cc_start: 0.8061 (m-80) cc_final: 0.7493 (m-80) REVERT: B 161 LEU cc_start: 0.8159 (mt) cc_final: 0.7794 (pt) REVERT: C 44 MET cc_start: 0.8074 (tpp) cc_final: 0.7631 (tpt) REVERT: C 348 TYR cc_start: 0.7810 (t80) cc_final: 0.7252 (t80) REVERT: C 354 TRP cc_start: 0.7473 (m100) cc_final: 0.6621 (m100) REVERT: C 419 MET cc_start: 0.7750 (mtt) cc_final: 0.7519 (ttm) REVERT: D 63 TRP cc_start: 0.8631 (m100) cc_final: 0.8335 (m100) REVERT: D 90 GLU cc_start: 0.8386 (tt0) cc_final: 0.8066 (pm20) REVERT: D 460 THR cc_start: 0.9107 (p) cc_final: 0.8817 (t) REVERT: D 465 ASN cc_start: 0.8614 (p0) cc_final: 0.8253 (p0) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.1970 time to fit residues: 28.5732 Evaluate side-chains 98 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 413 ASN D 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8469 Z= 0.207 Angle : 0.510 5.743 11869 Z= 0.257 Chirality : 0.037 0.176 1384 Planarity : 0.004 0.048 1229 Dihedral : 18.573 108.977 2116 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.46 % Allowed : 16.69 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 805 helix: 1.25 (0.31), residues: 274 sheet: -0.60 (0.46), residues: 132 loop : -0.18 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 63 HIS 0.001 0.000 HIS A 79 PHE 0.012 0.001 PHE A 233 TYR 0.016 0.001 TYR D 470 ARG 0.006 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7477 (mmt-90) cc_final: 0.7212 (mtp-110) REVERT: B 40 MET cc_start: 0.6515 (mtp) cc_final: 0.6061 (mtp) REVERT: B 59 GLN cc_start: 0.8231 (mp10) cc_final: 0.7777 (mp10) REVERT: B 124 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8481 (mmtp) REVERT: B 152 TYR cc_start: 0.8119 (m-80) cc_final: 0.7836 (m-80) REVERT: B 161 LEU cc_start: 0.8170 (mt) cc_final: 0.7808 (pt) REVERT: C 44 MET cc_start: 0.7985 (tpp) cc_final: 0.7556 (tpt) REVERT: C 348 TYR cc_start: 0.7858 (t80) cc_final: 0.7282 (t80) REVERT: C 413 ASN cc_start: 0.8000 (m-40) cc_final: 0.7754 (m110) REVERT: C 419 MET cc_start: 0.7787 (mtt) cc_final: 0.7552 (ttm) REVERT: D 63 TRP cc_start: 0.8626 (m100) cc_final: 0.8340 (m100) REVERT: D 90 GLU cc_start: 0.8411 (tt0) cc_final: 0.8091 (pm20) REVERT: D 460 THR cc_start: 0.9109 (p) cc_final: 0.8829 (t) REVERT: D 465 ASN cc_start: 0.8614 (p0) cc_final: 0.8233 (p0) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.1934 time to fit residues: 27.2083 Evaluate side-chains 97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8469 Z= 0.169 Angle : 0.493 5.776 11869 Z= 0.249 Chirality : 0.036 0.179 1384 Planarity : 0.004 0.048 1229 Dihedral : 18.562 108.661 2116 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.32 % Allowed : 16.98 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.33 (0.31), residues: 805 helix: 1.30 (0.31), residues: 274 sheet: -0.51 (0.47), residues: 132 loop : -0.20 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 63 HIS 0.002 0.000 HIS A 211 PHE 0.013 0.001 PHE A 233 TYR 0.016 0.001 TYR D 470 ARG 0.005 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7450 (mmt-90) cc_final: 0.7213 (mtp-110) REVERT: B 40 MET cc_start: 0.6443 (mtp) cc_final: 0.5964 (mtp) REVERT: B 59 GLN cc_start: 0.8202 (mp10) cc_final: 0.7772 (mp10) REVERT: B 124 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8470 (mmtp) REVERT: B 132 ASP cc_start: 0.8290 (t0) cc_final: 0.7765 (t0) REVERT: B 152 TYR cc_start: 0.8082 (m-80) cc_final: 0.7492 (m-80) REVERT: B 161 LEU cc_start: 0.8103 (mt) cc_final: 0.7743 (pt) REVERT: C 44 MET cc_start: 0.8042 (tpp) cc_final: 0.7600 (tpt) REVERT: C 348 TYR cc_start: 0.7851 (t80) cc_final: 0.7251 (t80) REVERT: C 354 TRP cc_start: 0.7638 (m100) cc_final: 0.6761 (m100) REVERT: C 413 ASN cc_start: 0.8017 (m-40) cc_final: 0.7773 (m110) REVERT: C 419 MET cc_start: 0.7738 (mtt) cc_final: 0.7480 (ttm) REVERT: D 63 TRP cc_start: 0.8610 (m100) cc_final: 0.8306 (m100) REVERT: D 90 GLU cc_start: 0.8378 (tt0) cc_final: 0.8055 (pm20) REVERT: D 460 THR cc_start: 0.9066 (p) cc_final: 0.8800 (t) REVERT: D 465 ASN cc_start: 0.8639 (p0) cc_final: 0.8261 (p0) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.1912 time to fit residues: 27.7038 Evaluate side-chains 101 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.158460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121890 restraints weight = 12481.467| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.45 r_work: 0.3465 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8469 Z= 0.216 Angle : 0.514 5.724 11869 Z= 0.260 Chirality : 0.037 0.180 1384 Planarity : 0.004 0.048 1229 Dihedral : 18.561 108.682 2116 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.32 % Allowed : 16.98 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.27 (0.31), residues: 805 helix: 1.26 (0.31), residues: 274 sheet: -0.49 (0.47), residues: 132 loop : -0.25 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 63 HIS 0.003 0.000 HIS A 211 PHE 0.028 0.001 PHE B 64 TYR 0.016 0.001 TYR D 470 ARG 0.005 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.19 seconds wall clock time: 35 minutes 37.69 seconds (2137.69 seconds total)