Starting phenix.real_space_refine on Sat Jul 26 17:23:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zu0_60477/07_2025/8zu0_60477_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zu0_60477/07_2025/8zu0_60477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zu0_60477/07_2025/8zu0_60477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zu0_60477/07_2025/8zu0_60477.map" model { file = "/net/cci-nas-00/data/ceres_data/8zu0_60477/07_2025/8zu0_60477_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zu0_60477/07_2025/8zu0_60477_trim.cif" } resolution = 3.16 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= 0.008 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 40 5.16 5 C 5460 2.51 5 N 1574 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 8752 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4323 Classifications: {'peptide': 554} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 1 Chain: "C" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4323 Classifications: {'peptide': 554} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 523} Chain breaks: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.58, per 1000 atoms: 0.87 Number of scatterers: 8752 At special positions: 0 Unit cell: (115.175, 98.175, 88.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 4 15.00 O 1674 8.00 N 1574 7.00 C 5460 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 44.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 56 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 100 through 114 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.869A pdb=" N GLN A 235 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.571A pdb=" N MET A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 376 through 396 Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 443 through 455 removed outlier: 5.470A pdb=" N GLU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 483 Processing helix chain 'A' and resid 490 through 498 removed outlier: 4.097A pdb=" N GLU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.625A pdb=" N LEU A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 548 through 567 removed outlier: 3.896A pdb=" N ASN A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 29 removed outlier: 3.528A pdb=" N GLY C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.868A pdb=" N GLN C 235 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.570A pdb=" N MET C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 376 through 396 removed outlier: 3.515A pdb=" N ALA C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'C' and resid 440 through 442 No H-bonds generated for 'chain 'C' and resid 440 through 442' Processing helix chain 'C' and resid 443 through 455 removed outlier: 5.476A pdb=" N GLU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 483 Processing helix chain 'C' and resid 490 through 498 removed outlier: 4.042A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.609A pdb=" N LEU C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'C' and resid 548 through 567 removed outlier: 3.896A pdb=" N ASN C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.519A pdb=" N THR A 32 " --> pdb=" O MET A 119 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE A 121 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU A 34 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 9 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 35 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 11 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 10 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 151 " --> pdb=" O PHE A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 removed outlier: 6.132A pdb=" N ALA A 94 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE A 83 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG A 96 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE A 81 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN A 98 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 131 removed outlier: 6.633A pdb=" N VAL A 139 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 128 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 137 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 130 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 135 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 171 removed outlier: 3.893A pdb=" N LYS A 162 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.766A pdb=" N ALA A 216 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 296 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 338 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP A 206 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 336 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.502A pdb=" N THR C 32 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE C 121 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C 34 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 151 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 52 removed outlier: 6.149A pdb=" N ALA C 94 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 83 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 96 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE C 81 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN C 98 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 131 removed outlier: 6.630A pdb=" N VAL C 139 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU C 128 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY C 137 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 130 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 135 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 168 through 171 removed outlier: 3.886A pdb=" N LYS C 162 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.771A pdb=" N ALA C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 296 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 338 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP C 206 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 336 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 484 through 485 384 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3022 1.34 - 1.46: 1313 1.46 - 1.57: 4501 1.57 - 1.69: 8 1.69 - 1.81: 74 Bond restraints: 8918 Sorted by residual: bond pdb=" C4 FAD A 601 " pdb=" O4 FAD A 601 " ideal model delta sigma weight residual 1.211 1.395 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C2 FAD A 601 " pdb=" O2 FAD A 601 " ideal model delta sigma weight residual 1.215 1.398 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C2 FAD C 601 " pdb=" O2 FAD C 601 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" C4 FAD C 601 " pdb=" O4 FAD C 601 " ideal model delta sigma weight residual 1.211 1.393 -0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C6A FAD C 601 " pdb=" N6A FAD C 601 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.00e-02 2.50e+03 3.29e+01 ... (remaining 8913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 12046 4.32 - 8.64: 34 8.64 - 12.95: 2 12.95 - 17.27: 0 17.27 - 21.59: 4 Bond angle restraints: 12086 Sorted by residual: angle pdb=" O1P FAD C 601 " pdb=" P FAD C 601 " pdb=" O2P FAD C 601 " ideal model delta sigma weight residual 122.50 100.91 21.59 3.00e+00 1.11e-01 5.18e+01 angle pdb=" O1P FAD A 601 " pdb=" P FAD A 601 " pdb=" O2P FAD A 601 " ideal model delta sigma weight residual 122.50 101.67 20.83 3.00e+00 1.11e-01 4.82e+01 angle pdb=" O1A FAD C 601 " pdb=" PA FAD C 601 " pdb=" O2A FAD C 601 " ideal model delta sigma weight residual 121.20 101.23 19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" O1A FAD A 601 " pdb=" PA FAD A 601 " pdb=" O2A FAD A 601 " ideal model delta sigma weight residual 121.20 101.29 19.91 3.00e+00 1.11e-01 4.41e+01 angle pdb=" N CYS C 47 " pdb=" CA CYS C 47 " pdb=" C CYS C 47 " ideal model delta sigma weight residual 112.12 116.74 -4.62 1.34e+00 5.57e-01 1.19e+01 ... (remaining 12081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 5200 26.91 - 53.81: 251 53.81 - 80.72: 34 80.72 - 107.62: 1 107.62 - 134.53: 2 Dihedral angle restraints: 5488 sinusoidal: 2312 harmonic: 3176 Sorted by residual: dihedral pdb=" O5' FAD A 601 " pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sinusoidal sigma weight residual -61.77 72.76 -134.53 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" O5' FAD C 601 " pdb=" O3P FAD C 601 " pdb=" P FAD C 601 " pdb=" PA FAD C 601 " ideal model delta sinusoidal sigma weight residual -61.77 71.21 -132.98 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CA THR C 375 " pdb=" C THR C 375 " pdb=" N GLY C 376 " pdb=" CA GLY C 376 " ideal model delta harmonic sigma weight residual -180.00 -164.81 -15.19 0 5.00e+00 4.00e-02 9.23e+00 ... (remaining 5485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1010 0.044 - 0.087: 244 0.087 - 0.131: 69 0.131 - 0.175: 5 0.175 - 0.218: 2 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C3B FAD C 601 " pdb=" C2B FAD C 601 " pdb=" C4B FAD C 601 " pdb=" O3B FAD C 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.50 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3B FAD A 601 " pdb=" C2B FAD A 601 " pdb=" C4B FAD A 601 " pdb=" O3B FAD A 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.51 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA CYS C 47 " pdb=" N CYS C 47 " pdb=" C CYS C 47 " pdb=" CB CYS C 47 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1327 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 3 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C 4 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 4 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 4 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 3 " 0.021 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 4 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 181 " 0.021 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 182 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " 0.018 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 61 2.51 - 3.10: 6798 3.10 - 3.70: 12876 3.70 - 4.30: 19124 4.30 - 4.90: 31875 Nonbonded interactions: 70734 Sorted by model distance: nonbonded pdb=" O2' FAD A 601 " pdb=" O4' FAD A 601 " model vdw 1.907 3.040 nonbonded pdb=" O2' FAD C 601 " pdb=" O4' FAD C 601 " model vdw 1.913 3.040 nonbonded pdb=" OG1 THR C 157 " pdb=" OG SER C 184 " model vdw 1.944 3.040 nonbonded pdb=" OG1 THR A 157 " pdb=" OG SER A 184 " model vdw 1.945 3.040 nonbonded pdb=" N ILE A 39 " pdb=" OE1 GLN A 122 " model vdw 2.039 3.120 ... (remaining 70729 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 7.290 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: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.120 Find NCS groups from input model: 0.290 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:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.008 0.184 8920 Z= 0.371 Angle : 0.776 21.591 12086 Z= 0.354 Chirality : 0.041 0.218 1330 Planarity : 0.004 0.034 1598 Dihedral : 15.114 134.526 3444 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 37.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.24 (0.26), residues: 1100 helix: 1.84 (0.25), residues: 432 sheet: 0.23 (0.38), residues: 172 loop : 0.24 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 484 HIS 0.011 0.002 HIS C 16 PHE 0.015 0.002 PHE C 366 TYR 0.014 0.002 TYR A 377 ARG 0.005 0.001 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.17514 ( 384) hydrogen bonds : angle 6.18135 ( 1080) covalent geometry : bond 0.00788 ( 8918) covalent geometry : angle 0.77639 (12086) Misc. bond : bond 0.00174 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.998 Fit side-chains REVERT: A 93 ARG cc_start: 0.7179 (ptp90) cc_final: 0.6961 (ptp90) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2106 time to fit residues: 33.1613 Evaluate side-chains 101 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.204623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148369 restraints weight = 9486.956| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.37 r_work: 0.3559 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8920 Z= 0.129 Angle : 0.579 7.127 12086 Z= 0.294 Chirality : 0.042 0.250 1330 Planarity : 0.004 0.044 1598 Dihedral : 9.965 103.291 1310 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.44 % Allowed : 4.82 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.48 (0.26), residues: 1100 helix: 2.10 (0.25), residues: 442 sheet: 0.04 (0.36), residues: 192 loop : 0.42 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 463 HIS 0.008 0.001 HIS C 37 PHE 0.009 0.001 PHE C 347 TYR 0.015 0.001 TYR C 520 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 384) hydrogen bonds : angle 4.78156 ( 1080) covalent geometry : bond 0.00279 ( 8918) covalent geometry : angle 0.57870 (12086) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.954 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 112 average time/residue: 0.2053 time to fit residues: 33.0655 Evaluate side-chains 105 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 86 optimal weight: 0.0020 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.200435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142926 restraints weight = 9716.561| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.41 r_work: 0.3553 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8920 Z= 0.121 Angle : 0.526 5.978 12086 Z= 0.268 Chirality : 0.041 0.183 1330 Planarity : 0.004 0.045 1598 Dihedral : 9.093 93.113 1310 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.88 % Allowed : 6.91 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.53 (0.26), residues: 1100 helix: 2.18 (0.25), residues: 442 sheet: 0.04 (0.37), residues: 192 loop : 0.43 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 463 HIS 0.003 0.001 HIS C 37 PHE 0.010 0.001 PHE C 347 TYR 0.012 0.001 TYR C 520 ARG 0.002 0.000 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 384) hydrogen bonds : angle 4.45627 ( 1080) covalent geometry : bond 0.00280 ( 8918) covalent geometry : angle 0.52633 (12086) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.066 Fit side-chains REVERT: C 518 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6858 (ppp) outliers start: 8 outliers final: 3 residues processed: 108 average time/residue: 0.2003 time to fit residues: 31.7108 Evaluate side-chains 104 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 75 optimal weight: 0.9980 chunk 104 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS C 123 GLN ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.202033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144717 restraints weight = 9628.791| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.41 r_work: 0.3566 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8920 Z= 0.103 Angle : 0.508 5.655 12086 Z= 0.257 Chirality : 0.040 0.171 1330 Planarity : 0.004 0.044 1598 Dihedral : 8.753 91.275 1310 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.66 % Allowed : 8.33 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.59 (0.26), residues: 1100 helix: 2.24 (0.25), residues: 442 sheet: 0.18 (0.38), residues: 192 loop : 0.39 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 484 HIS 0.003 0.001 HIS C 37 PHE 0.015 0.001 PHE C 347 TYR 0.011 0.001 TYR A 520 ARG 0.002 0.000 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 384) hydrogen bonds : angle 4.30210 ( 1080) covalent geometry : bond 0.00233 ( 8918) covalent geometry : angle 0.50793 (12086) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.858 Fit side-chains REVERT: A 417 LEU cc_start: 0.8172 (mt) cc_final: 0.7958 (mt) REVERT: A 518 MET cc_start: 0.7035 (ppp) cc_final: 0.6633 (ppp) REVERT: C 196 ARG cc_start: 0.7767 (tpt90) cc_final: 0.7496 (tpt170) REVERT: C 518 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6627 (ppp) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.2086 time to fit residues: 31.6948 Evaluate side-chains 111 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 13 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** 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 = 0.4317 r_free = 0.4317 target = 0.202330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145355 restraints weight = 9635.669| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.39 r_work: 0.3562 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8920 Z= 0.090 Angle : 0.484 4.954 12086 Z= 0.244 Chirality : 0.039 0.158 1330 Planarity : 0.004 0.044 1598 Dihedral : 8.528 91.127 1310 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.99 % Allowed : 8.99 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.67 (0.26), residues: 1100 helix: 2.32 (0.25), residues: 442 sheet: 0.37 (0.39), residues: 192 loop : 0.34 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 484 HIS 0.003 0.001 HIS C 37 PHE 0.008 0.001 PHE C 347 TYR 0.011 0.001 TYR A 520 ARG 0.002 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 384) hydrogen bonds : angle 4.14821 ( 1080) covalent geometry : bond 0.00199 ( 8918) covalent geometry : angle 0.48421 (12086) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 2.279 Fit side-chains REVERT: A 196 ARG cc_start: 0.7534 (mtp180) cc_final: 0.7321 (mtp180) REVERT: A 518 MET cc_start: 0.7221 (ppp) cc_final: 0.6788 (ppp) REVERT: C 196 ARG cc_start: 0.7789 (tpt90) cc_final: 0.7477 (tpt90) REVERT: C 518 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6735 (ppp) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 0.2500 time to fit residues: 40.9083 Evaluate side-chains 113 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.198229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140172 restraints weight = 9712.432| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.46 r_work: 0.3532 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8920 Z= 0.167 Angle : 0.557 5.752 12086 Z= 0.285 Chirality : 0.042 0.145 1330 Planarity : 0.004 0.044 1598 Dihedral : 8.771 94.502 1310 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.99 % Allowed : 10.42 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.40 (0.26), residues: 1100 helix: 2.10 (0.25), residues: 442 sheet: 0.16 (0.39), residues: 172 loop : 0.21 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 463 HIS 0.006 0.001 HIS C 16 PHE 0.014 0.002 PHE A 347 TYR 0.018 0.002 TYR A 377 ARG 0.003 0.000 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 384) hydrogen bonds : angle 4.37571 ( 1080) covalent geometry : bond 0.00401 ( 8918) covalent geometry : angle 0.55740 (12086) Misc. bond : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.7697 (mmm) cc_final: 0.7442 (mtp) REVERT: A 174 ARG cc_start: 0.5169 (ptp-170) cc_final: 0.4682 (ptp-170) REVERT: A 518 MET cc_start: 0.7197 (ppp) cc_final: 0.6723 (ppp) REVERT: C 417 LEU cc_start: 0.8170 (mt) cc_final: 0.7928 (mt) REVERT: C 518 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6726 (ppp) outliers start: 9 outliers final: 3 residues processed: 110 average time/residue: 0.2090 time to fit residues: 32.5108 Evaluate side-chains 112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** 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 = 0.4265 r_free = 0.4265 target = 0.196608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139467 restraints weight = 9792.860| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.37 r_work: 0.3545 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8920 Z= 0.148 Angle : 0.549 5.480 12086 Z= 0.276 Chirality : 0.041 0.155 1330 Planarity : 0.004 0.043 1598 Dihedral : 8.769 96.468 1310 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.55 % Allowed : 11.84 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.31 (0.26), residues: 1100 helix: 2.07 (0.25), residues: 442 sheet: -0.01 (0.39), residues: 172 loop : 0.17 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 401 HIS 0.005 0.001 HIS C 16 PHE 0.011 0.001 PHE A 367 TYR 0.014 0.002 TYR A 377 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 384) hydrogen bonds : angle 4.34276 ( 1080) covalent geometry : bond 0.00356 ( 8918) covalent geometry : angle 0.54947 (12086) Misc. bond : bond 0.00087 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 174 ARG cc_start: 0.5344 (ptp-170) cc_final: 0.4712 (ptp-170) REVERT: A 437 LEU cc_start: 0.5990 (tp) cc_final: 0.5730 (mm) REVERT: A 518 MET cc_start: 0.7185 (ppp) cc_final: 0.6705 (ppp) REVERT: C 417 LEU cc_start: 0.8146 (mt) cc_final: 0.7936 (mt) REVERT: C 518 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6913 (ppp) outliers start: 5 outliers final: 4 residues processed: 105 average time/residue: 0.2063 time to fit residues: 30.5231 Evaluate side-chains 109 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 42 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** 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 = 0.4281 r_free = 0.4281 target = 0.198181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140718 restraints weight = 9895.842| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.41 r_work: 0.3533 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8920 Z= 0.130 Angle : 0.535 6.442 12086 Z= 0.269 Chirality : 0.040 0.146 1330 Planarity : 0.004 0.044 1598 Dihedral : 8.680 98.342 1310 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.66 % Allowed : 11.62 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.33 (0.26), residues: 1100 helix: 2.10 (0.25), residues: 442 sheet: -0.00 (0.39), residues: 172 loop : 0.17 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 401 HIS 0.005 0.001 HIS C 16 PHE 0.009 0.001 PHE A 367 TYR 0.012 0.001 TYR A 377 ARG 0.002 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 384) hydrogen bonds : angle 4.25592 ( 1080) covalent geometry : bond 0.00309 ( 8918) covalent geometry : angle 0.53458 (12086) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.5152 (ptp-170) cc_final: 0.4608 (ptp-170) REVERT: A 437 LEU cc_start: 0.6069 (tp) cc_final: 0.5858 (mm) REVERT: A 518 MET cc_start: 0.7204 (ppp) cc_final: 0.6733 (ppp) REVERT: C 316 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5992 (mt) REVERT: C 518 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6916 (ppp) outliers start: 6 outliers final: 2 residues processed: 105 average time/residue: 0.2087 time to fit residues: 31.0519 Evaluate side-chains 107 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 104 optimal weight: 0.0370 chunk 47 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.200370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143445 restraints weight = 9802.436| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.39 r_work: 0.3584 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8920 Z= 0.100 Angle : 0.504 6.132 12086 Z= 0.251 Chirality : 0.039 0.149 1330 Planarity : 0.004 0.045 1598 Dihedral : 8.485 99.380 1310 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.66 % Allowed : 11.62 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.48 (0.26), residues: 1100 helix: 2.16 (0.25), residues: 446 sheet: 0.03 (0.38), residues: 192 loop : 0.36 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 401 HIS 0.003 0.001 HIS C 16 PHE 0.007 0.001 PHE C 367 TYR 0.012 0.001 TYR A 520 ARG 0.002 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 384) hydrogen bonds : angle 4.12945 ( 1080) covalent geometry : bond 0.00232 ( 8918) covalent geometry : angle 0.50355 (12086) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8428 (mtmm) REVERT: A 518 MET cc_start: 0.7243 (ppp) cc_final: 0.6808 (ppp) REVERT: C 316 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.5911 (mt) REVERT: C 437 LEU cc_start: 0.5838 (tp) cc_final: 0.5549 (mm) REVERT: C 518 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6853 (ppp) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.2063 time to fit residues: 31.0143 Evaluate side-chains 111 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 91 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.199965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143280 restraints weight = 9809.173| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.39 r_work: 0.3597 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8920 Z= 0.095 Angle : 0.505 8.766 12086 Z= 0.251 Chirality : 0.039 0.146 1330 Planarity : 0.004 0.046 1598 Dihedral : 8.367 100.332 1310 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.66 % Allowed : 12.06 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.59 (0.27), residues: 1100 helix: 2.22 (0.25), residues: 446 sheet: 0.18 (0.39), residues: 192 loop : 0.40 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 484 HIS 0.002 0.001 HIS A 219 PHE 0.009 0.001 PHE C 2 TYR 0.027 0.001 TYR A 520 ARG 0.002 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 384) hydrogen bonds : angle 4.05845 ( 1080) covalent geometry : bond 0.00217 ( 8918) covalent geometry : angle 0.50526 (12086) Misc. bond : bond 0.00027 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 518 MET cc_start: 0.7270 (ppp) cc_final: 0.6864 (ppp) REVERT: C 316 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5958 (mt) REVERT: C 437 LEU cc_start: 0.5791 (tp) cc_final: 0.5497 (mm) REVERT: C 481 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8245 (mtmm) REVERT: C 518 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6920 (ppp) outliers start: 6 outliers final: 2 residues processed: 107 average time/residue: 0.2179 time to fit residues: 33.5650 Evaluate side-chains 108 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.198101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140599 restraints weight = 9871.237| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.41 r_work: 0.3525 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8920 Z= 0.165 Angle : 0.574 8.911 12086 Z= 0.288 Chirality : 0.042 0.136 1330 Planarity : 0.004 0.045 1598 Dihedral : 8.656 102.377 1310 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.44 % Allowed : 12.06 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.29 (0.26), residues: 1100 helix: 2.02 (0.25), residues: 444 sheet: 0.04 (0.40), residues: 172 loop : 0.17 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 463 HIS 0.006 0.001 HIS C 16 PHE 0.013 0.001 PHE A 366 TYR 0.025 0.002 TYR C 520 ARG 0.003 0.000 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 384) hydrogen bonds : angle 4.32691 ( 1080) covalent geometry : bond 0.00401 ( 8918) covalent geometry : angle 0.57394 (12086) Misc. bond : bond 0.00102 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5819.07 seconds wall clock time: 100 minutes 27.01 seconds (6027.01 seconds total)