Starting phenix.real_space_refine on Fri Aug 22 16:57:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y72_33651/08_2025/7y72_33651.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y72_33651/08_2025/7y72_33651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y72_33651/08_2025/7y72_33651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y72_33651/08_2025/7y72_33651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y72_33651/08_2025/7y72_33651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y72_33651/08_2025/7y72_33651.map" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3920 2.51 5 N 1024 2.21 5 O 1193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1395 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1445 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "P" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1679 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain: "O" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1644 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 204} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU O 155 " occ=0.71 ... (7 atoms not shown) pdb=" OE2 GLU O 155 " occ=0.71 residue: pdb=" N VAL O 157 " occ=0.79 ... (5 atoms not shown) pdb=" CG2 VAL O 157 " occ=0.79 residue: pdb=" N SER O 186 " occ=0.78 ... (4 atoms not shown) pdb=" OG SER O 186 " occ=0.78 residue: pdb=" N ARG O 217 " occ=0.78 ... (9 atoms not shown) pdb=" NH2 ARG O 217 " occ=0.78 Time building chain proxies: 1.31, per 1000 atoms: 0.21 Number of scatterers: 6163 At special positions: 0 Unit cell: (98.345, 83.98, 119.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1193 8.00 N 1024 7.00 C 3920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 93 " distance=2.04 Simple disulfide: pdb=" SG CYS P 139 " - pdb=" SG CYS P 199 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.03 Simple disulfide: pdb=" SG CYS O 147 " - pdb=" SG CYS O 203 " distance=2.03 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: 0.44 Conformation dependent library (CDL) restraints added in 360.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 9.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.612A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.838A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.744A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.722A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.345A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.654A pdb=" N GLY P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.640A pdb=" N LYS O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'O' and resid 163 through 165 No H-bonds generated for 'chain 'O' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.921A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.703A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'P' and resid 5 through 7 removed outlier: 3.600A pdb=" N SER P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS P 23 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE P 76 " --> pdb=" O CYS P 23 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR P 74 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR P 77 " --> pdb=" O SER P 70 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER P 68 " --> pdb=" O LYS P 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.242A pdb=" N LEU P 11 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE P 53 " --> pdb=" O TRP P 40 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU P 42 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU P 51 " --> pdb=" O LEU P 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 119 through 123 removed outlier: 3.527A pdb=" N SER P 119 " --> pdb=" O ASN P 142 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL P 137 " --> pdb=" O LEU P 184 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR P 178 " --> pdb=" O ASN P 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 158 through 160 removed outlier: 4.767A pdb=" N TRP P 153 " --> pdb=" O GLN P 160 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS P 150 " --> pdb=" O THR P 202 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR P 202 " --> pdb=" O LYS P 150 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA P 198 " --> pdb=" O LYS P 154 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS P 199 " --> pdb=" O LYS P 212 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS P 212 " --> pdb=" O CYS P 199 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL P 201 " --> pdb=" O VAL P 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL P 210 " --> pdb=" O VAL P 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.563A pdb=" N LEU O 80 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.994A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR O 50 " --> pdb=" O ASN O 58 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 127 through 131 removed outlier: 3.659A pdb=" N GLY O 146 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 143 " --> pdb=" O VAL O 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP O 151 " --> pdb=" O TYR O 183 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR O 183 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 127 through 131 removed outlier: 3.659A pdb=" N GLY O 146 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 143 " --> pdb=" O VAL O 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP O 151 " --> pdb=" O TYR O 183 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR O 183 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 158 through 161 removed outlier: 3.982A pdb=" N THR O 158 " --> pdb=" O ASN O 206 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR O 201 " --> pdb=" O VAL O 218 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS O 203 " --> pdb=" O LYS O 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS O 216 " --> pdb=" O CYS O 203 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 396 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: 0.67 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1568 1.33 - 1.45: 1340 1.45 - 1.57: 3385 1.57 - 1.69: 0 1.69 - 1.82: 29 Bond restraints: 6322 Sorted by residual: bond pdb=" C PHE C 486 " pdb=" O PHE C 486 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.28e-02 6.10e+03 4.27e+00 bond pdb=" C GLU C 484 " pdb=" O GLU C 484 " ideal model delta sigma weight residual 1.235 1.211 0.025 1.26e-02 6.30e+03 3.87e+00 bond pdb=" CA PHE C 486 " pdb=" C PHE C 486 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.43e-02 4.89e+03 3.39e+00 bond pdb=" N ALA O 121 " pdb=" CA ALA O 121 " ideal model delta sigma weight residual 1.454 1.478 -0.025 1.34e-02 5.57e+03 3.35e+00 bond pdb=" N ARG P 113 " pdb=" CA ARG P 113 " ideal model delta sigma weight residual 1.455 1.476 -0.021 1.18e-02 7.18e+03 3.13e+00 ... (remaining 6317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 8376 1.79 - 3.58: 191 3.58 - 5.37: 27 5.37 - 7.15: 7 7.15 - 8.94: 2 Bond angle restraints: 8603 Sorted by residual: angle pdb=" N PHE C 486 " pdb=" CA PHE C 486 " pdb=" C PHE C 486 " ideal model delta sigma weight residual 112.87 106.77 6.10 1.20e+00 6.94e-01 2.58e+01 angle pdb=" C SER A 443 " pdb=" N LYS A 444 " pdb=" CA LYS A 444 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" N ARG P 66 " pdb=" CA ARG P 66 " pdb=" C ARG P 66 " ideal model delta sigma weight residual 114.56 109.14 5.42 1.27e+00 6.20e-01 1.82e+01 angle pdb=" N GLY C 485 " pdb=" CA GLY C 485 " pdb=" C GLY C 485 " ideal model delta sigma weight residual 112.73 117.62 -4.89 1.20e+00 6.94e-01 1.66e+01 angle pdb=" N ASN C 487 " pdb=" CA ASN C 487 " pdb=" C ASN C 487 " ideal model delta sigma weight residual 110.80 118.59 -7.79 2.13e+00 2.20e-01 1.34e+01 ... (remaining 8598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3420 17.79 - 35.58: 265 35.58 - 53.37: 46 53.37 - 71.16: 8 71.16 - 88.95: 6 Dihedral angle restraints: 3745 sinusoidal: 1441 harmonic: 2304 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 48.65 44.35 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -44.05 -41.95 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CA SER O 120 " pdb=" C SER O 120 " pdb=" N ALA O 121 " pdb=" CA ALA O 121 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 3742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 693 0.042 - 0.085: 154 0.085 - 0.127: 84 0.127 - 0.169: 5 0.169 - 0.212: 2 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA ASN C 487 " pdb=" N ASN C 487 " pdb=" C ASN C 487 " pdb=" CB ASN C 487 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LEU O 102 " pdb=" N LEU O 102 " pdb=" C LEU O 102 " pdb=" CB LEU O 102 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA ASN C 460 " pdb=" N ASN C 460 " pdb=" C ASN C 460 " pdb=" CB ASN C 460 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 935 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS P 112 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C LYS P 112 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS P 112 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG P 113 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O 120 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C SER O 120 " 0.068 2.00e-02 2.50e+03 pdb=" O SER O 120 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA O 121 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 484 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C GLU C 484 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU C 484 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY C 485 " -0.016 2.00e-02 2.50e+03 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 546 2.75 - 3.28: 5890 3.28 - 3.82: 9254 3.82 - 4.36: 10216 4.36 - 4.90: 18204 Nonbonded interactions: 44110 Sorted by model distance: nonbonded pdb=" OE1 GLN C 493 " pdb=" OD1 ASP P 75 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.224 3.040 nonbonded pdb=" O THR A 500 " pdb=" NE2 GLN A 506 " model vdw 2.267 3.120 nonbonded pdb=" OG1 THR C 478 " pdb=" ND2 ASN C 487 " model vdw 2.270 3.120 nonbonded pdb=" OE1 GLN A 414 " pdb=" ND2 ASN P 33 " model vdw 2.277 3.120 ... (remaining 44105 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 335 through 454 or (resid 455 and (name N or name CA or na \ me C or name O or name CB )) or resid 456 through 481 or resid 487 through 500 o \ r resid 503 through 515)) } 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=0.71 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.980 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 0.035 6330 Z= 0.150 Angle : 0.660 8.943 8619 Z= 0.367 Chirality : 0.045 0.212 938 Planarity : 0.005 0.042 1111 Dihedral : 13.270 88.951 2257 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.30 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.29), residues: 783 helix: -3.27 (0.49), residues: 57 sheet: 0.05 (0.36), residues: 243 loop : -1.90 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.017 0.001 TYR C 451 PHE 0.014 0.001 PHE C 456 TRP 0.007 0.001 TRP A 353 HIS 0.001 0.000 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6322) covalent geometry : angle 0.66038 ( 8603) SS BOND : bond 0.00303 ( 8) SS BOND : angle 0.60348 ( 16) hydrogen bonds : bond 0.29913 ( 152) hydrogen bonds : angle 10.81720 ( 396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8403 (pmt170) cc_final: 0.8106 (pmt170) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0852 time to fit residues: 13.3746 Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146547 restraints weight = 10946.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.147168 restraints weight = 8260.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.149406 restraints weight = 6031.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.149734 restraints weight = 4832.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149943 restraints weight = 4507.415| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6330 Z= 0.121 Angle : 0.597 8.747 8619 Z= 0.312 Chirality : 0.045 0.154 938 Planarity : 0.005 0.063 1111 Dihedral : 4.264 18.811 870 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.30), residues: 783 helix: -3.18 (0.54), residues: 53 sheet: 0.15 (0.34), residues: 251 loop : -1.64 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.014 0.001 TYR P 54 PHE 0.015 0.001 PHE C 456 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6322) covalent geometry : angle 0.59661 ( 8603) SS BOND : bond 0.00419 ( 8) SS BOND : angle 0.88814 ( 16) hydrogen bonds : bond 0.04729 ( 152) hydrogen bonds : angle 7.39768 ( 396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8464 (pmt170) cc_final: 0.8177 (pmt170) REVERT: P 65 ASP cc_start: 0.7245 (t0) cc_final: 0.6949 (t0) REVERT: P 150 LYS cc_start: 0.7357 (ttpt) cc_final: 0.7128 (ttpp) REVERT: O 19 SER cc_start: 0.8107 (m) cc_final: 0.7668 (p) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0939 time to fit residues: 14.0611 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 33 optimal weight: 6.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145973 restraints weight = 10832.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.145822 restraints weight = 8122.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148593 restraints weight = 6483.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148700 restraints weight = 4886.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149249 restraints weight = 4687.757| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6330 Z= 0.132 Angle : 0.585 8.779 8619 Z= 0.304 Chirality : 0.044 0.157 938 Planarity : 0.005 0.064 1111 Dihedral : 4.311 19.214 870 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.30), residues: 783 helix: -3.09 (0.56), residues: 53 sheet: 0.29 (0.34), residues: 253 loop : -1.65 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.015 0.001 TYR A 508 PHE 0.012 0.002 PHE A 497 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS P 194 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6322) covalent geometry : angle 0.58386 ( 8603) SS BOND : bond 0.00437 ( 8) SS BOND : angle 0.96175 ( 16) hydrogen bonds : bond 0.04146 ( 152) hydrogen bonds : angle 6.72677 ( 396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 150 LYS cc_start: 0.7219 (ttpt) cc_final: 0.7015 (ttpp) REVERT: O 19 SER cc_start: 0.8024 (m) cc_final: 0.7603 (p) REVERT: O 60 ASN cc_start: 0.8377 (t0) cc_final: 0.8176 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0926 time to fit residues: 14.3894 Evaluate side-chains 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 63 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.179047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144909 restraints weight = 10817.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145460 restraints weight = 8035.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147719 restraints weight = 6298.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.148212 restraints weight = 4543.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148404 restraints weight = 4284.313| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6330 Z= 0.115 Angle : 0.571 8.778 8619 Z= 0.294 Chirality : 0.044 0.160 938 Planarity : 0.005 0.047 1111 Dihedral : 4.235 17.890 870 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.30), residues: 783 helix: -3.15 (0.55), residues: 53 sheet: 0.38 (0.34), residues: 253 loop : -1.61 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 147 TYR 0.017 0.001 TYR C 423 PHE 0.011 0.001 PHE O 28 TRP 0.009 0.001 TRP C 436 HIS 0.001 0.001 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6322) covalent geometry : angle 0.56970 ( 8603) SS BOND : bond 0.00387 ( 8) SS BOND : angle 1.09521 ( 16) hydrogen bonds : bond 0.03450 ( 152) hydrogen bonds : angle 6.18549 ( 396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 150 LYS cc_start: 0.7386 (ttpt) cc_final: 0.7147 (ttpp) REVERT: O 19 SER cc_start: 0.7994 (m) cc_final: 0.7648 (p) REVERT: O 60 ASN cc_start: 0.8408 (t0) cc_final: 0.8175 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0902 time to fit residues: 14.3215 Evaluate side-chains 94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.179462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145711 restraints weight = 11002.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145051 restraints weight = 8222.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147729 restraints weight = 6378.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147989 restraints weight = 4878.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148391 restraints weight = 4737.443| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6330 Z= 0.121 Angle : 0.580 8.483 8619 Z= 0.299 Chirality : 0.044 0.159 938 Planarity : 0.005 0.045 1111 Dihedral : 4.241 18.702 870 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.30), residues: 783 helix: -3.04 (0.53), residues: 60 sheet: 0.41 (0.34), residues: 258 loop : -1.75 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 147 TYR 0.015 0.001 TYR A 369 PHE 0.018 0.001 PHE A 490 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6322) covalent geometry : angle 0.57878 ( 8603) SS BOND : bond 0.00368 ( 8) SS BOND : angle 0.97592 ( 16) hydrogen bonds : bond 0.03337 ( 152) hydrogen bonds : angle 6.02089 ( 396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 150 LYS cc_start: 0.7440 (ttpt) cc_final: 0.7172 (ttpp) REVERT: O 19 SER cc_start: 0.8063 (m) cc_final: 0.7645 (p) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0774 time to fit residues: 13.0659 Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.0270 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.179145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145617 restraints weight = 10878.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.146291 restraints weight = 7483.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148545 restraints weight = 6007.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148810 restraints weight = 4478.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.149202 restraints weight = 4331.440| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6330 Z= 0.120 Angle : 0.587 9.410 8619 Z= 0.301 Chirality : 0.045 0.158 938 Planarity : 0.005 0.046 1111 Dihedral : 4.219 18.476 870 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.15 % Allowed : 0.87 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.30), residues: 783 helix: -3.11 (0.52), residues: 60 sheet: 0.38 (0.34), residues: 259 loop : -1.72 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.018 0.001 TYR C 423 PHE 0.011 0.001 PHE A 490 TRP 0.008 0.001 TRP C 436 HIS 0.001 0.001 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6322) covalent geometry : angle 0.58609 ( 8603) SS BOND : bond 0.00359 ( 8) SS BOND : angle 0.88554 ( 16) hydrogen bonds : bond 0.03273 ( 152) hydrogen bonds : angle 5.90040 ( 396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 150 LYS cc_start: 0.7203 (ttpt) cc_final: 0.6976 (ttpp) REVERT: O 19 SER cc_start: 0.8011 (m) cc_final: 0.7663 (p) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.0898 time to fit residues: 14.9942 Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.178009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144418 restraints weight = 10955.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.143832 restraints weight = 8257.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146314 restraints weight = 6500.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146755 restraints weight = 4941.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.147156 restraints weight = 4576.433| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6330 Z= 0.136 Angle : 0.609 9.360 8619 Z= 0.312 Chirality : 0.045 0.157 938 Planarity : 0.005 0.048 1111 Dihedral : 4.320 18.863 870 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.29), residues: 783 helix: -3.09 (0.52), residues: 60 sheet: 0.42 (0.33), residues: 258 loop : -1.76 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 147 TYR 0.015 0.001 TYR A 369 PHE 0.013 0.001 PHE A 490 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6322) covalent geometry : angle 0.60789 ( 8603) SS BOND : bond 0.00393 ( 8) SS BOND : angle 0.91222 ( 16) hydrogen bonds : bond 0.03341 ( 152) hydrogen bonds : angle 5.88060 ( 396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.6976 (tp30) cc_final: 0.6568 (tp30) REVERT: P 150 LYS cc_start: 0.7316 (ttpt) cc_final: 0.7071 (ttpp) REVERT: O 19 SER cc_start: 0.8097 (m) cc_final: 0.7650 (p) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0897 time to fit residues: 14.4512 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.0020 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 76 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.181010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146625 restraints weight = 10891.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147674 restraints weight = 7946.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149819 restraints weight = 5822.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.150755 restraints weight = 4396.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.151041 restraints weight = 4139.047| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6330 Z= 0.110 Angle : 0.600 8.966 8619 Z= 0.306 Chirality : 0.044 0.155 938 Planarity : 0.005 0.047 1111 Dihedral : 4.201 19.315 870 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.21 % Rotamer: Outliers : 0.15 % Allowed : 0.44 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.29), residues: 783 helix: -3.10 (0.52), residues: 60 sheet: 0.47 (0.33), residues: 258 loop : -1.73 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 466 TYR 0.015 0.001 TYR A 369 PHE 0.010 0.001 PHE O 129 TRP 0.008 0.001 TRP A 353 HIS 0.001 0.000 HIS O 32 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6322) covalent geometry : angle 0.59932 ( 8603) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.84305 ( 16) hydrogen bonds : bond 0.03092 ( 152) hydrogen bonds : angle 5.69994 ( 396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 478 THR cc_start: 0.6046 (t) cc_final: 0.5266 (t) REVERT: P 150 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7222 (ttpp) REVERT: O 19 SER cc_start: 0.8004 (m) cc_final: 0.7645 (p) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.0876 time to fit residues: 14.4045 Evaluate side-chains 102 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146150 restraints weight = 10922.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147056 restraints weight = 7610.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148673 restraints weight = 6471.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.149575 restraints weight = 4560.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150163 restraints weight = 4132.310| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6330 Z= 0.122 Angle : 0.605 9.270 8619 Z= 0.310 Chirality : 0.044 0.154 938 Planarity : 0.005 0.049 1111 Dihedral : 4.204 19.187 870 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.56 % Favored : 91.32 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.29), residues: 783 helix: -3.01 (0.53), residues: 60 sheet: 0.49 (0.33), residues: 259 loop : -1.73 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.018 0.001 TYR A 495 PHE 0.015 0.001 PHE A 497 TRP 0.011 0.001 TRP A 353 HIS 0.001 0.001 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6322) covalent geometry : angle 0.60485 ( 8603) SS BOND : bond 0.00360 ( 8) SS BOND : angle 0.87654 ( 16) hydrogen bonds : bond 0.03164 ( 152) hydrogen bonds : angle 5.62758 ( 396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7016 (t80) cc_final: 0.6589 (t80) REVERT: C 478 THR cc_start: 0.6057 (t) cc_final: 0.5212 (t) REVERT: P 150 LYS cc_start: 0.7247 (ttpt) cc_final: 0.7040 (ttpp) REVERT: O 19 SER cc_start: 0.8104 (m) cc_final: 0.7656 (p) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.0988 time to fit residues: 16.0948 Evaluate side-chains 103 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 36 ASN O 162 ASN ** O 178 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 = 0.4223 r_free = 0.4223 target = 0.179720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146310 restraints weight = 10936.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146811 restraints weight = 7544.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148560 restraints weight = 6521.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149612 restraints weight = 4610.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149634 restraints weight = 4363.736| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6330 Z= 0.120 Angle : 0.614 9.209 8619 Z= 0.313 Chirality : 0.045 0.159 938 Planarity : 0.005 0.049 1111 Dihedral : 4.271 19.625 870 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.30 % Favored : 91.57 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.29), residues: 783 helix: -3.09 (0.53), residues: 60 sheet: 0.49 (0.33), residues: 259 loop : -1.72 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 466 TYR 0.017 0.001 TYR A 495 PHE 0.017 0.001 PHE A 497 TRP 0.009 0.001 TRP A 353 HIS 0.001 0.001 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6322) covalent geometry : angle 0.61370 ( 8603) SS BOND : bond 0.00368 ( 8) SS BOND : angle 0.86758 ( 16) hydrogen bonds : bond 0.03187 ( 152) hydrogen bonds : angle 5.58322 ( 396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 478 THR cc_start: 0.6095 (t) cc_final: 0.5297 (t) REVERT: P 150 LYS cc_start: 0.7280 (ttpt) cc_final: 0.7066 (ttpp) REVERT: O 19 SER cc_start: 0.8090 (m) cc_final: 0.7644 (p) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.0939 time to fit residues: 15.0587 Evaluate side-chains 107 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 36 ASN ** O 178 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 = 0.4210 r_free = 0.4210 target = 0.178746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145338 restraints weight = 10860.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144989 restraints weight = 7571.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147646 restraints weight = 6322.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148164 restraints weight = 4698.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.149073 restraints weight = 4726.657| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6330 Z= 0.131 Angle : 0.627 9.201 8619 Z= 0.321 Chirality : 0.045 0.154 938 Planarity : 0.005 0.050 1111 Dihedral : 4.355 19.248 870 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.07 % Favored : 90.80 % Rotamer: Outliers : 0.15 % Allowed : 0.44 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.29), residues: 783 helix: -3.05 (0.49), residues: 66 sheet: 0.49 (0.33), residues: 259 loop : -1.75 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 466 TYR 0.019 0.002 TYR P 37 PHE 0.018 0.002 PHE A 456 TRP 0.009 0.001 TRP A 353 HIS 0.001 0.001 HIS O 171 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6322) covalent geometry : angle 0.62594 ( 8603) SS BOND : bond 0.00401 ( 8) SS BOND : angle 0.94772 ( 16) hydrogen bonds : bond 0.03295 ( 152) hydrogen bonds : angle 5.62264 ( 396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.84 seconds wall clock time: 20 minutes 42.88 seconds (1242.88 seconds total)