Starting phenix.real_space_refine on Sat May 10 11:51:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y72_33651/05_2025/7y72_33651.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y72_33651/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y72_33651/05_2025/7y72_33651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y72_33651/05_2025/7y72_33651.map" model { file = "/net/cci-nas-00/data/ceres_data/7y72_33651/05_2025/7y72_33651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y72_33651/05_2025/7y72_33651.cif" } resolution = 4.03 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= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.71, per 1000 atoms: 0.76 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: 1.34 Conformation dependent library (CDL) restraints added in 902.3 milliseconds 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: 0.80 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: 1.87 Time building geometry restraints manager: 1.61 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- 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 (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: -1.99 (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 TRP 0.007 0.001 TRP A 353 HIS 0.001 0.000 HIS O 171 PHE 0.014 0.001 PHE C 456 TYR 0.017 0.001 TYR C 451 ARG 0.007 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.29913 ( 152) hydrogen bonds : angle 10.81720 ( 396) SS BOND : bond 0.00303 ( 8) SS BOND : angle 0.60348 ( 16) covalent geometry : bond 0.00295 ( 6322) covalent geometry : angle 0.66038 ( 8603) *********************** 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 : 0.726 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: 0.2204 time to fit residues: 34.7470 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 : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145230 restraints weight = 10825.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146057 restraints weight = 8233.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148215 restraints weight = 6384.077| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- 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 = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1157 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= 0.137 Angle : 0.614 8.960 8619 Z= 0.322 Chirality : 0.045 0.156 938 Planarity : 0.005 0.065 1111 Dihedral : 4.372 18.715 870 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % 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 (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: -1.72 (0.30), residues: 783 helix: -3.17 (0.54), residues: 53 sheet: 0.11 (0.35), residues: 243 loop : -1.64 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS O 171 PHE 0.015 0.002 PHE C 456 TYR 0.014 0.001 TYR P 54 ARG 0.004 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 152) hydrogen bonds : angle 7.54568 ( 396) SS BOND : bond 0.00503 ( 8) SS BOND : angle 0.97818 ( 16) covalent geometry : bond 0.00298 ( 6322) covalent geometry : angle 0.61309 ( 8603) *********************** 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 117 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 ASP cc_start: 0.7320 (t0) cc_final: 0.7091 (t0) REVERT: P 150 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6839 (ttpp) REVERT: O 19 SER cc_start: 0.8107 (m) cc_final: 0.7662 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2171 time to fit residues: 32.3330 Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.0970 chunk 60 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.182060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147483 restraints weight = 10865.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148832 restraints weight = 8293.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150851 restraints weight = 6381.395| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6330 Z= 0.110 Angle : 0.567 8.276 8619 Z= 0.294 Chirality : 0.044 0.155 938 Planarity : 0.005 0.050 1111 Dihedral : 4.183 19.065 870 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.56 (0.30), residues: 783 helix: -3.13 (0.56), residues: 53 sheet: 0.33 (0.34), residues: 253 loop : -1.62 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS P 194 PHE 0.015 0.001 PHE A 347 TYR 0.013 0.001 TYR A 369 ARG 0.004 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 152) hydrogen bonds : angle 6.55901 ( 396) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.83725 ( 16) covalent geometry : bond 0.00239 ( 6322) covalent geometry : angle 0.56614 ( 8603) *********************** 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 124 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8450 (pmt170) cc_final: 0.8177 (pmt170) REVERT: P 150 LYS cc_start: 0.7425 (ttpt) cc_final: 0.7208 (ttpp) REVERT: O 19 SER cc_start: 0.8007 (m) cc_final: 0.7597 (p) REVERT: O 60 ASN cc_start: 0.8312 (t0) cc_final: 0.8109 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2227 time to fit residues: 34.7175 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 : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.178391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143879 restraints weight = 10950.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144471 restraints weight = 8223.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146806 restraints weight = 6358.165| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1719 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= 0.130 Angle : 0.583 9.017 8619 Z= 0.301 Chirality : 0.044 0.160 938 Planarity : 0.005 0.060 1111 Dihedral : 4.284 18.531 870 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.64 (0.30), residues: 783 helix: -3.12 (0.53), residues: 60 sheet: 0.38 (0.34), residues: 253 loop : -1.74 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS O 171 PHE 0.011 0.001 PHE O 28 TYR 0.018 0.001 TYR A 423 ARG 0.004 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 152) hydrogen bonds : angle 6.21624 ( 396) SS BOND : bond 0.00396 ( 8) SS BOND : angle 1.09741 ( 16) covalent geometry : bond 0.00296 ( 6322) covalent geometry : angle 0.58159 ( 8603) *********************** 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 : 0.705 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: P 150 LYS cc_start: 0.7302 (ttpt) cc_final: 0.7074 (ttpp) REVERT: O 19 SER cc_start: 0.8013 (m) cc_final: 0.7661 (p) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2144 time to fit residues: 34.2452 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 : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 28 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.178896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144142 restraints weight = 10851.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145150 restraints weight = 8084.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147518 restraints weight = 6089.836| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6330 Z= 0.126 Angle : 0.581 8.433 8619 Z= 0.300 Chirality : 0.044 0.159 938 Planarity : 0.005 0.052 1111 Dihedral : 4.306 18.612 870 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % 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 (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: -1.64 (0.29), residues: 783 helix: -3.01 (0.54), residues: 60 sheet: 0.46 (0.34), residues: 253 loop : -1.80 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.001 HIS O 171 PHE 0.019 0.001 PHE A 490 TYR 0.018 0.001 TYR A 423 ARG 0.005 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 152) hydrogen bonds : angle 6.04796 ( 396) SS BOND : bond 0.00392 ( 8) SS BOND : angle 1.02485 ( 16) covalent geometry : bond 0.00287 ( 6322) covalent geometry : angle 0.58009 ( 8603) *********************** 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 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.697 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: 0.7376 (ttpt) cc_final: 0.7121 (ttpp) REVERT: O 19 SER cc_start: 0.8073 (m) cc_final: 0.7649 (p) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1971 time to fit residues: 32.1857 Evaluate side-chains 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.0070 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 171 GLN O 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.177014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143244 restraints weight = 10817.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144381 restraints weight = 7574.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145778 restraints weight = 6417.131| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2118 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= 0.150 Angle : 0.609 9.593 8619 Z= 0.316 Chirality : 0.045 0.158 938 Planarity : 0.005 0.048 1111 Dihedral : 4.460 19.159 870 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.54 (0.30), residues: 783 helix: -2.93 (0.57), residues: 53 sheet: 0.37 (0.34), residues: 258 loop : -1.68 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS O 171 PHE 0.015 0.002 PHE A 490 TYR 0.015 0.001 TYR A 369 ARG 0.005 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 152) hydrogen bonds : angle 6.02513 ( 396) SS BOND : bond 0.00417 ( 8) SS BOND : angle 1.00102 ( 16) covalent geometry : bond 0.00341 ( 6322) covalent geometry : angle 0.60764 ( 8603) *********************** 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 133 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.682 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: 0.7017 (t80) cc_final: 0.6231 (t80) REVERT: P 129 GLN cc_start: 0.7159 (mm110) cc_final: 0.6847 (mm110) REVERT: P 150 LYS cc_start: 0.7307 (ttpt) cc_final: 0.7047 (ttpp) REVERT: O 19 SER cc_start: 0.8106 (m) cc_final: 0.7696 (p) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2096 time to fit residues: 35.8398 Evaluate side-chains 102 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 53 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.178243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144052 restraints weight = 10917.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.146190 restraints weight = 7975.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148217 restraints weight = 5833.300| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2189 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= 0.128 Angle : 0.610 9.157 8619 Z= 0.312 Chirality : 0.045 0.166 938 Planarity : 0.005 0.045 1111 Dihedral : 4.361 19.220 870 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.15 % Allowed : 1.16 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.55 (0.29), residues: 783 helix: -2.98 (0.56), residues: 53 sheet: 0.37 (0.33), residues: 259 loop : -1.69 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS O 207 PHE 0.014 0.001 PHE A 456 TYR 0.015 0.001 TYR A 369 ARG 0.006 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 152) hydrogen bonds : angle 5.90312 ( 396) SS BOND : bond 0.00361 ( 8) SS BOND : angle 0.99511 ( 16) covalent geometry : bond 0.00293 ( 6322) covalent geometry : angle 0.60933 ( 8603) *********************** 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: 1 poor density : 124 time to evaluate : 0.711 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: 0.7160 (t80) cc_final: 0.6256 (t80) REVERT: A 465 GLU cc_start: 0.7025 (tp30) cc_final: 0.6571 (tp30) REVERT: C 478 THR cc_start: 0.6007 (t) cc_final: 0.5213 (t) REVERT: P 146 PRO cc_start: 0.8909 (Cg_exo) cc_final: 0.8645 (Cg_endo) REVERT: P 150 LYS cc_start: 0.7228 (ttpt) cc_final: 0.6959 (ttpp) REVERT: O 19 SER cc_start: 0.8082 (m) cc_final: 0.7632 (p) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2113 time to fit residues: 33.6759 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.177147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142607 restraints weight = 10771.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143836 restraints weight = 8066.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145716 restraints weight = 5984.787| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2367 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= 0.137 Angle : 0.625 9.356 8619 Z= 0.321 Chirality : 0.045 0.158 938 Planarity : 0.005 0.045 1111 Dihedral : 4.412 19.320 870 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.32 % Favored : 90.55 % 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 (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 (0.29), residues: 783 helix: -3.02 (0.54), residues: 53 sheet: 0.37 (0.33), residues: 258 loop : -1.73 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.002 0.001 HIS O 171 PHE 0.014 0.002 PHE A 456 TYR 0.015 0.001 TYR A 369 ARG 0.007 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 152) hydrogen bonds : angle 5.89206 ( 396) SS BOND : bond 0.00456 ( 8) SS BOND : angle 1.02976 ( 16) covalent geometry : bond 0.00316 ( 6322) covalent geometry : angle 0.62448 ( 8603) *********************** 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 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.755 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: A 351 TYR cc_start: 0.7156 (t80) cc_final: 0.6355 (t80) REVERT: C 478 THR cc_start: 0.6024 (t) cc_final: 0.5209 (t) REVERT: P 146 PRO cc_start: 0.8857 (Cg_exo) cc_final: 0.8588 (Cg_endo) REVERT: P 150 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6973 (ttpp) REVERT: P 166 GLU cc_start: 0.7379 (pm20) cc_final: 0.7173 (pm20) REVERT: O 19 SER cc_start: 0.8125 (m) cc_final: 0.7680 (p) REVERT: O 201 TYR cc_start: 0.6251 (m-80) cc_final: 0.5843 (m-80) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.2025 time to fit residues: 33.8144 Evaluate side-chains 105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ** 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 = 0.4197 r_free = 0.4197 target = 0.177580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143500 restraints weight = 10948.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143521 restraints weight = 8183.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145955 restraints weight = 5978.104| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6330 Z= 0.134 Angle : 0.629 9.101 8619 Z= 0.322 Chirality : 0.045 0.157 938 Planarity : 0.005 0.044 1111 Dihedral : 4.410 19.698 870 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.56 % Favored : 91.32 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.64 (0.29), residues: 783 helix: -3.03 (0.54), residues: 60 sheet: 0.40 (0.33), residues: 259 loop : -1.78 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.001 0.001 HIS O 32 PHE 0.011 0.001 PHE A 400 TYR 0.016 0.001 TYR C 423 ARG 0.006 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 152) hydrogen bonds : angle 5.81982 ( 396) SS BOND : bond 0.00406 ( 8) SS BOND : angle 0.89803 ( 16) covalent geometry : bond 0.00312 ( 6322) covalent geometry : angle 0.62823 ( 8603) *********************** 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 : 0.700 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: A 465 GLU cc_start: 0.7082 (tp30) cc_final: 0.6676 (tp30) REVERT: P 128 GLU cc_start: 0.6006 (tm-30) cc_final: 0.5806 (tm-30) REVERT: P 146 PRO cc_start: 0.8829 (Cg_exo) cc_final: 0.8565 (Cg_endo) REVERT: O 19 SER cc_start: 0.8121 (m) cc_final: 0.7665 (p) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.2097 time to fit residues: 34.2572 Evaluate side-chains 104 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.173351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139857 restraints weight = 11129.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139728 restraints weight = 8283.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142062 restraints weight = 6658.670| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6330 Z= 0.202 Angle : 0.702 9.851 8619 Z= 0.366 Chirality : 0.048 0.174 938 Planarity : 0.006 0.046 1111 Dihedral : 4.942 21.610 870 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.86 % Favored : 89.02 % 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 (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: -1.94 (0.29), residues: 783 helix: -3.02 (0.50), residues: 66 sheet: 0.17 (0.33), residues: 258 loop : -1.98 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.002 0.001 HIS O 171 PHE 0.023 0.002 PHE A 490 TYR 0.021 0.002 TYR P 37 ARG 0.006 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 152) hydrogen bonds : angle 6.13778 ( 396) SS BOND : bond 0.00585 ( 8) SS BOND : angle 1.23080 ( 16) covalent geometry : bond 0.00474 ( 6322) covalent geometry : angle 0.70070 ( 8603) ********************** 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 125 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.7255 (tp30) cc_final: 0.6444 (tp30) REVERT: C 478 THR cc_start: 0.6140 (t) cc_final: 0.5203 (t) REVERT: C 487 ASN cc_start: 0.7463 (t0) cc_final: 0.7179 (t0) REVERT: P 146 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8510 (Cg_endo) REVERT: O 150 LYS cc_start: 0.4673 (mmmt) cc_final: 0.4262 (tppt) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2269 time to fit residues: 35.5062 Evaluate side-chains 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 36 ASN P 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142140 restraints weight = 11065.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142515 restraints weight = 8330.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144257 restraints weight = 7067.227| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6330 Z= 0.159 Angle : 0.670 9.296 8619 Z= 0.347 Chirality : 0.046 0.158 938 Planarity : 0.005 0.045 1111 Dihedral : 4.785 19.494 870 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.20 % Favored : 90.68 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.93 (0.29), residues: 783 helix: -3.07 (0.53), residues: 60 sheet: 0.11 (0.33), residues: 258 loop : -1.95 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.001 0.001 HIS O 171 PHE 0.016 0.002 PHE A 490 TYR 0.017 0.002 TYR A 351 ARG 0.004 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 152) hydrogen bonds : angle 6.03158 ( 396) SS BOND : bond 0.00475 ( 8) SS BOND : angle 1.09918 ( 16) covalent geometry : bond 0.00373 ( 6322) covalent geometry : angle 0.66926 ( 8603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.66 seconds wall clock time: 40 minutes 36.19 seconds (2436.19 seconds total)