Starting phenix.real_space_refine on Fri Dec 27 17:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y72_33651/12_2024/7y72_33651.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y72_33651/12_2024/7y72_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_33651/12_2024/7y72_33651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y72_33651/12_2024/7y72_33651.map" model { file = "/net/cci-nas-00/data/ceres_data/7y72_33651/12_2024/7y72_33651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y72_33651/12_2024/7y72_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-5532/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: 4.47, per 1000 atoms: 0.73 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: 1.37 Conformation dependent library (CDL) restraints added in 876.8 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: 0.71 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: 1.67 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: 0.010 Normalize map: mean=0, sd=1: 3.850 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.650 Find NCS groups from input model: 0.120 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- 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 6322 Z= 0.187 Angle : 0.660 8.943 8603 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 *********************** 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 : 0.695 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: 0.2131 time to fit residues: 33.6949 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 : 0.800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 6322 Z= 0.191 Angle : 0.613 8.960 8603 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 *********************** 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 : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 ASP cc_start: 0.7304 (t0) cc_final: 0.7075 (t0) REVERT: P 150 LYS cc_start: 0.7037 (ttpt) cc_final: 0.6718 (ttpp) REVERT: O 19 SER cc_start: 0.8090 (m) cc_final: 0.7651 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2184 time to fit residues: 32.5659 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 : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6322 Z= 0.254 Angle : 0.622 8.983 8603 Z= 0.326 Chirality : 0.045 0.156 938 Planarity : 0.005 0.051 1111 Dihedral : 4.630 19.128 870 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -1.74 (0.30), residues: 783 helix: -3.03 (0.58), residues: 53 sheet: 0.14 (0.33), residues: 258 loop : -1.76 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 436 HIS 0.003 0.001 HIS P 194 PHE 0.015 0.002 PHE A 497 TYR 0.019 0.002 TYR A 508 ARG 0.004 0.001 ARG A 466 *********************** 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 : 0.687 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: 0.7143 (t80) cc_final: 0.6273 (t80) REVERT: P 65 ASP cc_start: 0.7378 (t0) cc_final: 0.7059 (t0) REVERT: P 150 LYS cc_start: 0.7242 (ttpt) cc_final: 0.7036 (ttpp) REVERT: O 19 SER cc_start: 0.8022 (m) cc_final: 0.7588 (p) REVERT: O 60 ASN cc_start: 0.8493 (t0) cc_final: 0.8287 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2184 time to fit residues: 33.7944 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 : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6322 Z= 0.166 Angle : 0.583 8.391 8603 Z= 0.302 Chirality : 0.044 0.160 938 Planarity : 0.005 0.049 1111 Dihedral : 4.437 19.868 870 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % 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 (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: -1.74 (0.29), residues: 783 helix: -3.09 (0.54), residues: 60 sheet: 0.28 (0.34), residues: 253 loop : -1.79 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.001 HIS O 171 PHE 0.017 0.001 PHE A 490 TYR 0.017 0.001 TYR C 423 ARG 0.004 0.000 ARG A 466 *********************** 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 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 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: O 19 SER cc_start: 0.7955 (m) cc_final: 0.7613 (p) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2302 time to fit residues: 38.2900 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.0000 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6322 Z= 0.224 Angle : 0.608 9.642 8603 Z= 0.316 Chirality : 0.045 0.163 938 Planarity : 0.005 0.048 1111 Dihedral : 4.521 19.359 870 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 (0.57), residues: 53 sheet: 0.22 (0.33), residues: 259 loop : -1.69 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS O 171 PHE 0.014 0.002 PHE P 67 TYR 0.015 0.002 TYR A 369 ARG 0.005 0.000 ARG A 466 *********************** 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 129 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.728 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: 0.6868 (tp30) cc_final: 0.6417 (tp30) REVERT: O 19 SER cc_start: 0.8061 (m) cc_final: 0.7609 (p) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2219 time to fit residues: 36.2379 Evaluate side-chains 101 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6322 Z= 0.202 Angle : 0.611 9.180 8603 Z= 0.315 Chirality : 0.045 0.159 938 Planarity : 0.005 0.047 1111 Dihedral : 4.469 19.410 870 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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 (0.57), residues: 53 sheet: 0.26 (0.33), residues: 258 loop : -1.71 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.001 0.001 HIS O 171 PHE 0.012 0.001 PHE O 28 TYR 0.016 0.001 TYR C 423 ARG 0.004 0.000 ARG A 466 *********************** 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 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.647 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: 0.6913 (tp30) cc_final: 0.6471 (tp30) REVERT: O 19 SER cc_start: 0.8002 (m) cc_final: 0.7634 (p) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2142 time to fit residues: 34.8558 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 : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.0060 chunk 47 optimal weight: 0.0980 chunk 45 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN P 152 GLN O 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6322 Z= 0.146 Angle : 0.581 8.447 8603 Z= 0.297 Chirality : 0.044 0.155 938 Planarity : 0.005 0.045 1111 Dihedral : 4.169 19.254 870 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.28 % Favored : 92.59 % Rotamer: Outliers : 0.29 % Allowed : 1.16 % Favored : 98.55 % 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: -1.51 (0.30), residues: 783 helix: -3.14 (0.54), residues: 53 sheet: 0.39 (0.33), residues: 259 loop : -1.63 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.001 0.000 HIS O 207 PHE 0.011 0.001 PHE O 28 TYR 0.011 0.001 TYR O 201 ARG 0.007 0.000 ARG A 466 *********************** 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 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.720 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: C 478 THR cc_start: 0.6145 (t) cc_final: 0.5360 (t) REVERT: O 19 SER cc_start: 0.8059 (m) cc_final: 0.7617 (p) REVERT: O 199 GLN cc_start: 0.7127 (tm-30) cc_final: 0.6837 (tm-30) REVERT: O 201 TYR cc_start: 0.5900 (m-80) cc_final: 0.5461 (m-80) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.2050 time to fit residues: 34.1934 Evaluate side-chains 100 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 36 ASN O 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6322 Z= 0.298 Angle : 0.669 9.593 8603 Z= 0.348 Chirality : 0.046 0.159 938 Planarity : 0.006 0.077 1111 Dihedral : 4.725 21.161 870 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.98 % Favored : 88.89 % Rotamer: Outliers : 0.15 % Allowed : 0.73 % Favored : 99.13 % 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: -1.81 (0.29), residues: 783 helix: -3.00 (0.54), residues: 60 sheet: 0.28 (0.33), residues: 256 loop : -1.91 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.003 0.001 HIS O 171 PHE 0.018 0.002 PHE A 490 TYR 0.036 0.002 TYR P 37 ARG 0.005 0.001 ARG A 466 *********************** 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 : 0.722 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: A 465 GLU cc_start: 0.7073 (tp30) cc_final: 0.6580 (tp30) REVERT: C 478 THR cc_start: 0.6114 (t) cc_final: 0.5308 (t) REVERT: O 199 GLN cc_start: 0.7202 (tm-30) cc_final: 0.6799 (tm-30) REVERT: O 201 TYR cc_start: 0.5984 (m-80) cc_final: 0.5551 (m-80) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2365 time to fit residues: 38.3729 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 : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.0030 chunk 51 optimal weight: 10.0000 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6322 Z= 0.192 Angle : 0.630 9.093 8603 Z= 0.324 Chirality : 0.046 0.189 938 Planarity : 0.005 0.069 1111 Dihedral : 4.509 21.341 870 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.30 % Favored : 91.57 % Rotamer: Outliers : 0.15 % Allowed : 0.58 % 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: -1.79 (0.29), residues: 783 helix: -2.99 (0.55), residues: 60 sheet: 0.31 (0.33), residues: 259 loop : -1.93 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.001 0.001 HIS P 194 PHE 0.022 0.002 PHE C 429 TYR 0.017 0.002 TYR A 423 ARG 0.004 0.000 ARG C 346 *********************** 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 129 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.683 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: A 465 GLU cc_start: 0.6968 (tp30) cc_final: 0.6517 (tp30) REVERT: C 478 THR cc_start: 0.6092 (t) cc_final: 0.5266 (t) REVERT: O 19 SER cc_start: 0.8106 (m) cc_final: 0.7612 (p) REVERT: O 199 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6830 (tm-30) REVERT: O 201 TYR cc_start: 0.5990 (m-80) cc_final: 0.5624 (m-80) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2229 time to fit residues: 36.2094 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 : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6322 Z= 0.215 Angle : 0.644 9.251 8603 Z= 0.332 Chirality : 0.046 0.157 938 Planarity : 0.005 0.065 1111 Dihedral : 4.619 21.149 870 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.45 % Favored : 90.42 % 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: -1.76 (0.29), residues: 783 helix: -3.06 (0.54), residues: 53 sheet: 0.25 (0.33), residues: 259 loop : -1.86 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.001 0.001 HIS P 194 PHE 0.023 0.002 PHE C 429 TYR 0.020 0.002 TYR C 423 ARG 0.004 0.001 ARG C 346 ********************** 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 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.714 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: 0.6961 (tp30) cc_final: 0.6498 (tp30) REVERT: C 478 THR cc_start: 0.5994 (t) cc_final: 0.5142 (t) REVERT: O 19 SER cc_start: 0.8071 (m) cc_final: 0.7605 (p) REVERT: O 199 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6806 (tm-30) REVERT: O 201 TYR cc_start: 0.5958 (m-80) cc_final: 0.5612 (m-80) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2254 time to fit residues: 36.6777 Evaluate side-chains 104 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.0470 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 0.4880 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.177676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144995 restraints weight = 10840.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144519 restraints weight = 7833.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.147102 restraints weight = 6645.656| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- 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 = 0.71 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 = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6322 Z= 0.166 Angle : 0.619 8.797 8603 Z= 0.318 Chirality : 0.045 0.160 938 Planarity : 0.005 0.060 1111 Dihedral : 4.424 22.164 870 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.21 % 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: -1.79 (0.29), residues: 783 helix: -3.09 (0.52), residues: 60 sheet: 0.33 (0.33), residues: 259 loop : -1.93 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS O 171 PHE 0.013 0.001 PHE A 456 TYR 0.011 0.001 TYR P 37 ARG 0.004 0.001 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.69 seconds wall clock time: 32 minutes 42.99 seconds (1962.99 seconds total)