Starting phenix.real_space_refine on Sat Aug 23 15:17:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qh0_53151/08_2025/9qh0_53151.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qh0_53151/08_2025/9qh0_53151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qh0_53151/08_2025/9qh0_53151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qh0_53151/08_2025/9qh0_53151.map" model { file = "/net/cci-nas-00/data/ceres_data/9qh0_53151/08_2025/9qh0_53151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qh0_53151/08_2025/9qh0_53151.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 64 5.16 5 C 8099 2.51 5 N 2278 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12946 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4180 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 25, 'TRANS': 523} Chain: "B" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4180 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 25, 'TRANS': 523} Chain: "C" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4168 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 523} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 411 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 8, 'TRANS': 46} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.73, per 1000 atoms: 0.21 Number of scatterers: 12946 At special positions: 0 Unit cell: (90.52, 113.15, 108.04, 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 64 16.00 O 2505 8.00 N 2278 7.00 C 8099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 420.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 38.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 85 through 100 Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 125 through 141 removed outlier: 4.408A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.575A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 239 through 258 removed outlier: 5.900A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 289 through 312 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 397 through 413 removed outlier: 4.266A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.580A pdb=" N ALA A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 515 through 539 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 85 through 100 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 125 through 141 removed outlier: 4.439A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 227 removed outlier: 3.587A pdb=" N ALA B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 213 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 5.871A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 3.562A pdb=" N ARG B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 311 Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.526A pdb=" N ALA B 362 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 397 through 412 Processing helix chain 'B' and resid 437 through 454 removed outlier: 3.552A pdb=" N VAL B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 541 removed outlier: 3.510A pdb=" N MET B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 Processing helix chain 'C' and resid 85 through 100 Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 125 through 142 removed outlier: 4.220A pdb=" N VAL C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.768A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 239 through 258 removed outlier: 5.985A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 Processing helix chain 'C' and resid 289 through 311 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.573A pdb=" N VAL C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 412 removed outlier: 3.611A pdb=" N GLY C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 437 through 453 Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.734A pdb=" N GLN C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 541 " --> pdb=" O MET C 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1046 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 6.327A pdb=" N ALA A 39 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.614A pdb=" N GLY A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 156 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 175 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N GLU A 190 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 10.159A pdb=" N ASP A 508 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N GLU A 192 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N GLN A 506 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N GLN A 194 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALA A 504 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.212A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU A 433 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN A 349 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 11 removed outlier: 6.198A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 163 removed outlier: 4.152A pdb=" N TYR B 156 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 175 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N GLU B 190 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ASP B 508 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N GLU B 192 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLN B 506 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLN B 194 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ALA B 504 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 324 removed outlier: 3.612A pdb=" N THR D1011 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 381 removed outlier: 6.402A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU B 433 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN B 349 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 363 through 367 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 11 removed outlier: 6.143A pdb=" N ALA C 39 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 160 through 163 removed outlier: 4.085A pdb=" N TYR C 156 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 175 " --> pdb=" O TYR C 156 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N GLU C 190 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ASP C 508 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N GLU C 192 " --> pdb=" O GLN C 506 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLN C 506 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N GLN C 194 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ALA C 504 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 504 " --> pdb=" O ALA C 496 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 327 through 331 removed outlier: 6.156A pdb=" N GLN C 349 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 363 through 366 748 hydrogen bonds defined for protein. 2037 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: 1.66 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4446 1.34 - 1.45: 1410 1.45 - 1.57: 7164 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 13145 Sorted by residual: bond pdb=" CB VAL B 179 " pdb=" CG2 VAL B 179 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CG MET A 466 " pdb=" SD MET A 466 " ideal model delta sigma weight residual 1.803 1.767 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CG LEU A 310 " pdb=" CD1 LEU A 310 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CB PRO A 314 " pdb=" CG PRO A 314 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.79e+00 bond pdb=" CG MET B 466 " pdb=" SD MET B 466 " ideal model delta sigma weight residual 1.803 1.771 0.032 2.50e-02 1.60e+03 1.60e+00 ... (remaining 13140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 17380 2.03 - 4.06: 390 4.06 - 6.09: 43 6.09 - 8.12: 3 8.12 - 10.15: 1 Bond angle restraints: 17817 Sorted by residual: angle pdb=" CA LEU B 177 " pdb=" CB LEU B 177 " pdb=" CG LEU B 177 " ideal model delta sigma weight residual 116.30 126.45 -10.15 3.50e+00 8.16e-02 8.41e+00 angle pdb=" CA GLN B 520 " pdb=" CB GLN B 520 " pdb=" CG GLN B 520 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.22e+00 angle pdb=" N ASN C 524 " pdb=" CA ASN C 524 " pdb=" C ASN C 524 " ideal model delta sigma weight residual 111.69 108.25 3.44 1.23e+00 6.61e-01 7.83e+00 angle pdb=" CA MET A 466 " pdb=" CB MET A 466 " pdb=" CG MET A 466 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.45e+00 angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 112.10 107.24 4.86 1.82e+00 3.02e-01 7.14e+00 ... (remaining 17812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 7217 16.69 - 33.37: 626 33.37 - 50.06: 148 50.06 - 66.74: 25 66.74 - 83.43: 21 Dihedral angle restraints: 8037 sinusoidal: 3191 harmonic: 4846 Sorted by residual: dihedral pdb=" CD ARG A 83 " pdb=" NE ARG A 83 " pdb=" CZ ARG A 83 " pdb=" NH1 ARG A 83 " ideal model delta sinusoidal sigma weight residual 0.00 -81.48 81.48 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CD ARG C 259 " pdb=" NE ARG C 259 " pdb=" CZ ARG C 259 " pdb=" NH1 ARG C 259 " ideal model delta sinusoidal sigma weight residual 0.00 -68.28 68.28 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CD ARG B 545 " pdb=" NE ARG B 545 " pdb=" CZ ARG B 545 " pdb=" NH1 ARG B 545 " ideal model delta sinusoidal sigma weight residual 0.00 -68.24 68.24 1 1.00e+01 1.00e-02 6.04e+01 ... (remaining 8034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1418 0.045 - 0.089: 473 0.089 - 0.133: 143 0.133 - 0.178: 14 0.178 - 0.222: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA MET A 466 " pdb=" N MET A 466 " pdb=" C MET A 466 " pdb=" CB MET A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TYR B 258 " pdb=" N TYR B 258 " pdb=" C TYR B 258 " pdb=" CB TYR B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE B 548 " pdb=" N ILE B 548 " pdb=" C ILE B 548 " pdb=" CB ILE B 548 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 2049 not shown) Planarity restraints: 2366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 83 " 0.943 9.50e-02 1.11e+02 4.24e-01 1.18e+02 pdb=" NE ARG A 83 " -0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 83 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG A 83 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 83 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 259 " 0.861 9.50e-02 1.11e+02 3.87e-01 1.02e+02 pdb=" NE ARG C 259 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG C 259 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG C 259 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG C 259 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 545 " 0.849 9.50e-02 1.11e+02 3.82e-01 1.01e+02 pdb=" NE ARG B 545 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG B 545 " 0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG B 545 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 545 " 0.001 2.00e-02 2.50e+03 ... (remaining 2363 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1153 2.74 - 3.28: 12193 3.28 - 3.82: 21362 3.82 - 4.36: 25944 4.36 - 4.90: 45356 Nonbonded interactions: 106008 Sorted by model distance: nonbonded pdb=" OE2 GLU A 430 " pdb=" OH TYR B 68 " model vdw 2.199 3.040 nonbonded pdb=" O ILE A 260 " pdb=" NH1 ARG A 266 " model vdw 2.231 3.120 nonbonded pdb=" OH TYR C 258 " pdb=" OE2 GLU C 301 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OD1 ASP A 159 " model vdw 2.267 3.040 nonbonded pdb=" O VAL B 179 " pdb=" NE2 GLN B 212 " model vdw 2.289 3.120 ... (remaining 106003 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' and (resid 1 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 549)) selection = (chain 'B' and (resid 1 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 549)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.220 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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: 0.020 Load rotamer database and sin/cos tables:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.005 0.067 13145 Z= 0.201 Angle : 0.700 10.153 17817 Z= 0.384 Chirality : 0.048 0.222 2052 Planarity : 0.022 0.424 2366 Dihedral : 14.003 83.431 4923 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1694 helix: 0.96 (0.22), residues: 561 sheet: 1.25 (0.25), residues: 399 loop : -0.58 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.005 ARG B 545 TYR 0.041 0.002 TYR C 11 PHE 0.043 0.002 PHE C 493 TRP 0.007 0.001 TRP C 231 HIS 0.007 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00464 (13145) covalent geometry : angle 0.70018 (17817) hydrogen bonds : bond 0.12801 ( 748) hydrogen bonds : angle 5.33940 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6695 (pmm) cc_final: 0.6294 (mtt) REVERT: A 19 GLU cc_start: 0.8342 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 389 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 405 ARG cc_start: 0.8148 (tpt-90) cc_final: 0.7708 (tpp80) REVERT: A 512 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 83 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6932 (ppt-90) REVERT: B 201 MET cc_start: 0.9196 (mmm) cc_final: 0.8869 (mmt) REVERT: B 484 ASP cc_start: 0.7971 (m-30) cc_final: 0.7660 (m-30) REVERT: C 192 GLU cc_start: 0.8167 (pt0) cc_final: 0.7958 (pt0) outliers start: 0 outliers final: 3 residues processed: 218 average time/residue: 0.6261 time to fit residues: 146.4377 Evaluate side-chains 149 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain C residue 172 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.0000 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.076093 restraints weight = 19723.726| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.76 r_work: 0.2822 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13145 Z= 0.122 Angle : 0.531 6.703 17817 Z= 0.279 Chirality : 0.043 0.154 2052 Planarity : 0.005 0.045 2366 Dihedral : 4.244 29.473 1843 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.46 % Allowed : 10.41 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.21), residues: 1694 helix: 2.11 (0.22), residues: 567 sheet: 1.62 (0.25), residues: 399 loop : -0.17 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 259 TYR 0.014 0.001 TYR A 11 PHE 0.023 0.002 PHE A 493 TRP 0.005 0.001 TRP C 233 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00266 (13145) covalent geometry : angle 0.53112 (17817) hydrogen bonds : bond 0.04131 ( 748) hydrogen bonds : angle 4.19555 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.571 Fit side-chains REVERT: A 1 MET cc_start: 0.6745 (pmm) cc_final: 0.6209 (mtt) REVERT: A 19 GLU cc_start: 0.8521 (tt0) cc_final: 0.7822 (tm-30) REVERT: A 389 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 405 ARG cc_start: 0.8021 (tpt-90) cc_final: 0.7484 (tpp80) REVERT: A 508 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: A 512 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8247 (mt-10) REVERT: B 83 ARG cc_start: 0.7481 (ptt180) cc_final: 0.7000 (ppt-90) REVERT: B 484 ASP cc_start: 0.8218 (m-30) cc_final: 0.7910 (m-30) REVERT: C 192 GLU cc_start: 0.8247 (pt0) cc_final: 0.8001 (pt0) REVERT: C 430 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7401 (mp0) outliers start: 20 outliers final: 8 residues processed: 165 average time/residue: 0.6138 time to fit residues: 109.0592 Evaluate side-chains 154 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 1019 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 148 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN B 13 GLN C 209 HIS C 239 ASN D1004 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.071500 restraints weight = 19846.707| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.75 r_work: 0.2637 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13145 Z= 0.236 Angle : 0.575 6.056 17817 Z= 0.304 Chirality : 0.046 0.151 2052 Planarity : 0.005 0.070 2366 Dihedral : 4.421 27.688 1838 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.89 % Allowed : 11.35 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.21), residues: 1694 helix: 2.42 (0.22), residues: 564 sheet: 1.97 (0.25), residues: 423 loop : -0.04 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 399 TYR 0.024 0.002 TYR A 11 PHE 0.021 0.002 PHE C 493 TRP 0.010 0.002 TRP A 233 HIS 0.008 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00562 (13145) covalent geometry : angle 0.57529 (17817) hydrogen bonds : bond 0.04842 ( 748) hydrogen bonds : angle 4.17312 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8926 (tt0) cc_final: 0.8257 (tt0) REVERT: A 83 ARG cc_start: 0.8215 (tpp-160) cc_final: 0.7977 (mmp80) REVERT: A 86 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: A 389 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8129 (mm-30) REVERT: B 466 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8369 (mtm) REVERT: B 484 ASP cc_start: 0.8609 (m-30) cc_final: 0.8346 (m-30) REVERT: C 239 ASN cc_start: 0.6965 (t0) cc_final: 0.6634 (t0) REVERT: C 369 MET cc_start: 0.8655 (mmm) cc_final: 0.8378 (mmm) REVERT: C 430 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 492 ASP cc_start: 0.8294 (t70) cc_final: 0.7842 (t70) outliers start: 26 outliers final: 6 residues processed: 164 average time/residue: 0.6146 time to fit residues: 108.3662 Evaluate side-chains 148 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 430 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 70 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 0.1980 chunk 39 optimal weight: 0.0010 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN C 54 GLN D1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.075038 restraints weight = 19690.621| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.76 r_work: 0.2704 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13145 Z= 0.100 Angle : 0.472 7.635 17817 Z= 0.247 Chirality : 0.042 0.156 2052 Planarity : 0.004 0.037 2366 Dihedral : 3.961 20.030 1836 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.75 % Allowed : 13.03 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.21), residues: 1694 helix: 2.82 (0.22), residues: 567 sheet: 1.98 (0.26), residues: 396 loop : 0.03 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 360 TYR 0.016 0.001 TYR A 267 PHE 0.013 0.001 PHE A 493 TRP 0.004 0.001 TRP A 231 HIS 0.003 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00212 (13145) covalent geometry : angle 0.47207 (17817) hydrogen bonds : bond 0.03432 ( 748) hydrogen bonds : angle 3.84453 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.385 Fit side-chains REVERT: A 19 GLU cc_start: 0.8760 (tt0) cc_final: 0.8081 (tt0) REVERT: A 267 TYR cc_start: 0.7426 (m-10) cc_final: 0.7178 (m-80) REVERT: B 399 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7098 (ptm-80) REVERT: B 481 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8463 (pp) REVERT: B 484 ASP cc_start: 0.8481 (m-30) cc_final: 0.8264 (m-30) REVERT: C 49 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8093 (mppt) REVERT: C 83 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7813 (mmp-170) REVERT: C 239 ASN cc_start: 0.7000 (t0) cc_final: 0.6669 (t0) REVERT: C 256 ASP cc_start: 0.8679 (t70) cc_final: 0.8195 (t70) REVERT: C 430 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: C 492 ASP cc_start: 0.8125 (t70) cc_final: 0.7781 (t70) outliers start: 24 outliers final: 4 residues processed: 159 average time/residue: 0.6475 time to fit residues: 110.5053 Evaluate side-chains 145 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 486 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 159 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN C 520 GLN D1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.072872 restraints weight = 19769.198| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.75 r_work: 0.2663 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13145 Z= 0.150 Angle : 0.493 6.279 17817 Z= 0.258 Chirality : 0.043 0.152 2052 Planarity : 0.004 0.039 2366 Dihedral : 3.995 19.643 1836 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.67 % Allowed : 14.05 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.21), residues: 1694 helix: 2.91 (0.22), residues: 567 sheet: 2.00 (0.26), residues: 399 loop : 0.08 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 360 TYR 0.015 0.002 TYR B 380 PHE 0.017 0.001 PHE C 493 TRP 0.004 0.001 TRP A 233 HIS 0.005 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00350 (13145) covalent geometry : angle 0.49333 (17817) hydrogen bonds : bond 0.03846 ( 748) hydrogen bonds : angle 3.85036 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.532 Fit side-chains REVERT: A 19 GLU cc_start: 0.8937 (tt0) cc_final: 0.8237 (tt0) REVERT: A 466 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: B 471 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: B 481 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8579 (pp) REVERT: B 484 ASP cc_start: 0.8588 (m-30) cc_final: 0.8377 (m-30) REVERT: C 49 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8154 (mppt) REVERT: C 239 ASN cc_start: 0.6950 (t0) cc_final: 0.6617 (t0) REVERT: C 249 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7576 (tt) REVERT: C 256 ASP cc_start: 0.8732 (t70) cc_final: 0.8251 (t70) REVERT: C 430 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: C 466 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: C 492 ASP cc_start: 0.8320 (t70) cc_final: 0.7943 (t70) outliers start: 23 outliers final: 5 residues processed: 147 average time/residue: 0.6390 time to fit residues: 101.2591 Evaluate side-chains 147 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 486 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 152 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 542 ASN D1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.099080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.070516 restraints weight = 19669.127| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.72 r_work: 0.2627 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13145 Z= 0.209 Angle : 0.534 6.575 17817 Z= 0.279 Chirality : 0.045 0.155 2052 Planarity : 0.004 0.046 2366 Dihedral : 4.201 20.700 1836 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.89 % Allowed : 13.90 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.21), residues: 1694 helix: 2.83 (0.22), residues: 564 sheet: 1.96 (0.26), residues: 399 loop : 0.08 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 360 TYR 0.020 0.002 TYR C 380 PHE 0.017 0.001 PHE B 493 TRP 0.005 0.001 TRP C 231 HIS 0.005 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00493 (13145) covalent geometry : angle 0.53366 (17817) hydrogen bonds : bond 0.04433 ( 748) hydrogen bonds : angle 3.96836 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.463 Fit side-chains REVERT: A 19 GLU cc_start: 0.8978 (tt0) cc_final: 0.8311 (tt0) REVERT: A 466 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8455 (mtm) REVERT: B 399 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6980 (ptm-80) REVERT: B 471 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: C 49 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8361 (mppt) REVERT: C 83 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8084 (mmp-170) REVERT: C 239 ASN cc_start: 0.7022 (t0) cc_final: 0.6698 (t0) REVERT: C 430 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: C 466 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: C 492 ASP cc_start: 0.8337 (t70) cc_final: 0.7934 (t70) outliers start: 26 outliers final: 5 residues processed: 154 average time/residue: 0.6629 time to fit residues: 109.7603 Evaluate side-chains 146 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 123 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 0.0270 chunk 161 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1004 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.073049 restraints weight = 19519.401| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.73 r_work: 0.2669 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13145 Z= 0.104 Angle : 0.475 6.835 17817 Z= 0.248 Chirality : 0.042 0.155 2052 Planarity : 0.004 0.050 2366 Dihedral : 3.979 20.464 1836 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.24 % Allowed : 15.36 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.21), residues: 1694 helix: 3.05 (0.21), residues: 567 sheet: 1.97 (0.26), residues: 399 loop : 0.18 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 360 TYR 0.014 0.001 TYR C 267 PHE 0.012 0.001 PHE C 493 TRP 0.003 0.000 TRP D1028 HIS 0.003 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00229 (13145) covalent geometry : angle 0.47515 (17817) hydrogen bonds : bond 0.03553 ( 748) hydrogen bonds : angle 3.77993 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.437 Fit side-chains REVERT: A 19 GLU cc_start: 0.8945 (tt0) cc_final: 0.8224 (tt0) REVERT: A 86 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: B 399 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6877 (ptm-80) REVERT: C 49 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8286 (mppt) REVERT: C 83 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8097 (mmp-170) REVERT: C 239 ASN cc_start: 0.6995 (t0) cc_final: 0.6665 (t0) REVERT: C 430 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 466 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8288 (mtm) REVERT: C 492 ASP cc_start: 0.8291 (t70) cc_final: 0.7927 (t70) REVERT: D 1051 SER cc_start: 0.9072 (p) cc_final: 0.8680 (m) outliers start: 17 outliers final: 3 residues processed: 142 average time/residue: 0.6833 time to fit residues: 104.2131 Evaluate side-chains 144 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 34 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1004 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.071829 restraints weight = 19542.395| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.72 r_work: 0.2653 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13145 Z= 0.146 Angle : 0.495 6.690 17817 Z= 0.258 Chirality : 0.043 0.166 2052 Planarity : 0.004 0.058 2366 Dihedral : 3.998 20.416 1836 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.38 % Allowed : 15.65 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.21), residues: 1694 helix: 3.05 (0.21), residues: 567 sheet: 1.98 (0.26), residues: 399 loop : 0.17 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 360 TYR 0.015 0.002 TYR B 380 PHE 0.015 0.001 PHE C 493 TRP 0.003 0.001 TRP D1028 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00341 (13145) covalent geometry : angle 0.49455 (17817) hydrogen bonds : bond 0.03798 ( 748) hydrogen bonds : angle 3.79989 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.474 Fit side-chains REVERT: A 19 GLU cc_start: 0.8966 (tt0) cc_final: 0.8281 (tt0) REVERT: B 399 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6957 (ptm-80) REVERT: C 49 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8374 (mppt) REVERT: C 83 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8138 (mmp-170) REVERT: C 239 ASN cc_start: 0.7079 (t0) cc_final: 0.6751 (t0) REVERT: C 249 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7683 (tt) REVERT: C 430 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: C 466 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: C 492 ASP cc_start: 0.8309 (t70) cc_final: 0.7969 (t70) REVERT: D 1051 SER cc_start: 0.9081 (p) cc_final: 0.8677 (m) outliers start: 19 outliers final: 6 residues processed: 144 average time/residue: 0.6645 time to fit residues: 103.0716 Evaluate side-chains 144 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1004 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.071292 restraints weight = 19528.158| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.72 r_work: 0.2640 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13145 Z= 0.169 Angle : 0.506 6.038 17817 Z= 0.264 Chirality : 0.043 0.152 2052 Planarity : 0.004 0.062 2366 Dihedral : 4.070 20.559 1836 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.16 % Allowed : 15.87 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.21), residues: 1694 helix: 3.03 (0.21), residues: 567 sheet: 1.97 (0.26), residues: 399 loop : 0.14 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 360 TYR 0.017 0.002 TYR C 380 PHE 0.016 0.001 PHE C 493 TRP 0.004 0.001 TRP D1028 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00398 (13145) covalent geometry : angle 0.50551 (17817) hydrogen bonds : bond 0.03990 ( 748) hydrogen bonds : angle 3.84294 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.431 Fit side-chains REVERT: A 19 GLU cc_start: 0.8959 (tt0) cc_final: 0.8274 (tt0) REVERT: A 86 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: B 399 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6981 (ptm-80) REVERT: C 49 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8374 (mppt) REVERT: C 83 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8158 (mmp-170) REVERT: C 239 ASN cc_start: 0.7076 (t0) cc_final: 0.6793 (t0) REVERT: C 249 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7657 (tt) REVERT: C 430 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: C 466 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: C 492 ASP cc_start: 0.8301 (t70) cc_final: 0.7938 (t70) REVERT: D 1051 SER cc_start: 0.9093 (p) cc_final: 0.8682 (m) outliers start: 16 outliers final: 7 residues processed: 142 average time/residue: 0.6879 time to fit residues: 104.6846 Evaluate side-chains 145 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 486 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1004 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.069908 restraints weight = 19609.295| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.73 r_work: 0.2615 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13145 Z= 0.242 Angle : 0.544 6.968 17817 Z= 0.284 Chirality : 0.045 0.159 2052 Planarity : 0.005 0.066 2366 Dihedral : 4.202 20.834 1836 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.24 % Allowed : 15.57 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.21), residues: 1694 helix: 2.92 (0.21), residues: 567 sheet: 1.93 (0.26), residues: 399 loop : 0.08 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 360 TYR 0.020 0.002 TYR C 380 PHE 0.020 0.002 PHE B 493 TRP 0.006 0.001 TRP D1028 HIS 0.010 0.001 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00580 (13145) covalent geometry : angle 0.54353 (17817) hydrogen bonds : bond 0.04411 ( 748) hydrogen bonds : angle 3.92789 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.498 Fit side-chains REVERT: A 19 GLU cc_start: 0.9018 (tt0) cc_final: 0.8363 (tt0) REVERT: A 86 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: B 399 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7011 (ptm-80) REVERT: C 49 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8400 (mppt) REVERT: C 83 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8170 (mmp-170) REVERT: C 239 ASN cc_start: 0.7132 (t0) cc_final: 0.6828 (t0) REVERT: C 430 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: C 466 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8269 (mtm) REVERT: C 492 ASP cc_start: 0.8369 (t70) cc_final: 0.7991 (t70) outliers start: 17 outliers final: 6 residues processed: 141 average time/residue: 0.6634 time to fit residues: 100.2025 Evaluate side-chains 144 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 149 optimal weight: 0.0050 chunk 79 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 61 optimal weight: 0.0040 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 HIS D1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.073144 restraints weight = 19596.164| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.73 r_work: 0.2677 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13145 Z= 0.105 Angle : 0.488 11.848 17817 Z= 0.252 Chirality : 0.042 0.155 2052 Planarity : 0.004 0.060 2366 Dihedral : 3.947 20.374 1836 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.02 % Allowed : 15.87 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.21), residues: 1694 helix: 3.14 (0.21), residues: 567 sheet: 2.05 (0.26), residues: 396 loop : 0.16 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 360 TYR 0.015 0.001 TYR C 267 PHE 0.013 0.001 PHE B 493 TRP 0.003 0.000 TRP D1028 HIS 0.004 0.000 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00234 (13145) covalent geometry : angle 0.48799 (17817) hydrogen bonds : bond 0.03397 ( 748) hydrogen bonds : angle 3.73816 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4155.16 seconds wall clock time: 71 minutes 22.80 seconds (4282.80 seconds total)