Starting phenix.real_space_refine on Fri Oct 23 01:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nah_49194/10_2026/9nah_49194.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nah_49194/10_2026/9nah_49194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nah_49194/10_2026/9nah_49194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nah_49194/10_2026/9nah_49194.map" model { file = "/net/cci-nas-00/data/ceres_data/9nah_49194/10_2026/9nah_49194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nah_49194/10_2026/9nah_49194.cif" } resolution = 3.64 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 15 5.16 5 C 4597 2.51 5 N 1219 2.21 5 O 1346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7180 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5296 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'PTRANS': 17, 'TRANS': 727} Chain breaks: 2 Unresolved non-hydrogen bonds: 833 Unresolved non-hydrogen angles: 1028 Unresolved non-hydrogen dihedrals: 707 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 24, 'ARG:plan': 21, 'GLU:plan': 37, 'GLN:plan1': 8, 'HIS:plan': 8, 'ASN:plan1': 16, 'TYR:plan': 12, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 568 Chain: "C" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1853 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 7, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 17, 'ASN:plan1': 5, 'PHE:plan': 5, 'ASP:plan': 9, 'ARG:plan': 7, 'TYR:plan': 5, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 257 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.56, per 1000 atoms: 0.22 Number of scatterers: 7180 At special positions: 0 Unit cell: (73.04, 97.68, 117.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 3 15.00 O 1346 8.00 N 1219 7.00 C 4597 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: 0.42 Conformation dependent library (CDL) restraints added in 472.4 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 45.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.950A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.937A pdb=" N THR A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 34 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.500A pdb=" N SER A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.996A pdb=" N LYS A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.918A pdb=" N ILE A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.829A pdb=" N ILE A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 328 through 337 removed outlier: 3.919A pdb=" N ASP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.684A pdb=" N ILE A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.922A pdb=" N LYS A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 402 through 410 removed outlier: 4.159A pdb=" N ASP A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 removed outlier: 3.880A pdb=" N GLU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 removed outlier: 3.740A pdb=" N PHE A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 509 through 518 removed outlier: 4.470A pdb=" N LEU A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.653A pdb=" N HIS A 528 " --> pdb=" O HIS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.645A pdb=" N SER A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.677A pdb=" N THR A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 621 through 628 removed outlier: 3.569A pdb=" N ILE A 625 " --> pdb=" O PHE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 634 removed outlier: 4.148A pdb=" N ARG A 634 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.624A pdb=" N ALA A 644 " --> pdb=" O TRP A 640 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 4.344A pdb=" N GLU A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 695 removed outlier: 3.652A pdb=" N TYR A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 removed outlier: 4.024A pdb=" N SER A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 removed outlier: 3.705A pdb=" N ASP A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'C' and resid 11 through 21 removed outlier: 3.799A pdb=" N PHE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 59 removed outlier: 3.701A pdb=" N GLU C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 59 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.591A pdb=" N ILE C 68 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C 69 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 removed outlier: 3.511A pdb=" N MET C 86 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 removed outlier: 3.712A pdb=" N ILE C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.650A pdb=" N ASN C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 removed outlier: 4.344A pdb=" N ARG C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 4.767A pdb=" N ALA C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 268 Processing helix chain 'C' and resid 269 through 274 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.573A pdb=" N TYR A 235 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE A 208 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 236 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 210 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 25 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 143 removed outlier: 4.104A pdb=" N LEU A 143 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 288 removed outlier: 6.232A pdb=" N GLU A 287 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 424 through 425 removed outlier: 3.884A pdb=" N GLY A 347 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 346 " --> pdb=" O ILE A 448 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 126 removed outlier: 5.428A pdb=" N LYS C 141 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS C 162 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU C 143 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 210 through 211 removed outlier: 3.753A pdb=" N LEU C 236 " --> pdb=" O PHE C 210 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C 235 " --> pdb=" O ILE C 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 229 hydrogen bonds defined for protein. 648 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: 1.09 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2360 1.34 - 1.46: 1541 1.46 - 1.58: 3379 1.58 - 1.69: 8 1.69 - 1.81: 22 Bond restraints: 7310 Sorted by residual: bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.702 -0.258 1.10e-02 8.26e+03 5.49e+02 bond pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " ideal model delta sigma weight residual 1.526 1.302 0.224 1.10e-02 8.26e+03 4.13e+02 bond pdb=" C6 ATP A 801 " pdb=" N6 ATP A 801 " ideal model delta sigma weight residual 1.337 1.486 -0.149 1.10e-02 8.26e+03 1.84e+02 bond pdb=" C2' ATP A 801 " pdb=" O2' ATP A 801 " ideal model delta sigma weight residual 1.423 1.292 0.131 1.30e-02 5.92e+03 1.02e+02 bond pdb=" C1' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.416 1.309 0.107 1.30e-02 5.92e+03 6.82e+01 ... (remaining 7305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 9918 3.44 - 6.89: 67 6.89 - 10.33: 9 10.33 - 13.78: 1 13.78 - 17.22: 1 Bond angle restraints: 9996 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 122.65 17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 123.82 13.01 1.00e+00 1.00e+00 1.69e+02 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.99 7.81 1.00e+00 1.00e+00 6.10e+01 angle pdb=" N1 ATP A 801 " pdb=" C2 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 128.69 121.41 7.28 1.00e+00 1.00e+00 5.30e+01 angle pdb=" N3 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N9 ATP A 801 " ideal model delta sigma weight residual 127.04 134.87 -7.83 1.15e+00 7.59e-01 4.65e+01 ... (remaining 9991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4053 17.91 - 35.82: 224 35.82 - 53.73: 39 53.73 - 71.63: 15 71.63 - 89.54: 2 Dihedral angle restraints: 4333 sinusoidal: 1326 harmonic: 3007 Sorted by residual: dihedral pdb=" CA SER A 214 " pdb=" C SER A 214 " pdb=" N LEU A 215 " pdb=" CA LEU A 215 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ASP A 397 " pdb=" C ASP A 397 " pdb=" N SER A 398 " pdb=" CA SER A 398 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA THR A 64 " pdb=" C THR A 64 " pdb=" N GLN A 65 " pdb=" CA GLN A 65 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1043 0.057 - 0.113: 168 0.113 - 0.170: 9 0.170 - 0.227: 3 0.227 - 0.284: 3 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE A 254 " pdb=" CA ILE A 254 " pdb=" CG1 ILE A 254 " pdb=" CG2 ILE A 254 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1223 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 562 " -0.042 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 563 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 151 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C ARG C 151 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG C 151 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU C 152 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 481 " 0.022 2.00e-02 2.50e+03 1.64e-02 4.68e+00 pdb=" CG PHE A 481 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 481 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 481 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 481 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 481 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 481 " 0.010 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 824 2.75 - 3.29: 7489 3.29 - 3.82: 11243 3.82 - 4.36: 12773 4.36 - 4.90: 21531 Nonbonded interactions: 53860 Sorted by model distance: nonbonded pdb=" O TYR A 626 " pdb=" OH TYR A 639 " model vdw 2.211 3.040 nonbonded pdb=" O CYS A 213 " pdb=" OH TYR A 235 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A 600 " pdb=" OH TYR A 633 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 605 " pdb=" OD1 ASP A 607 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASN A 720 " pdb=" N SER A 721 " model vdw 2.308 3.120 ... (remaining 53855 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 7.530 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 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 : 0.006 0.258 7310 Z= 0.491 Angle : 0.747 17.223 9996 Z= 0.458 Chirality : 0.044 0.284 1226 Planarity : 0.004 0.065 1279 Dihedral : 12.600 89.542 2367 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % 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 are not related in a simple way. whole: -2.57 (0.27), residues: 1008 helix: -0.77 (0.26), residues: 418 sheet: -3.23 (0.51), residues: 90 loop : -2.22 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 151 TYR 0.014 0.001 TYR A 626 PHE 0.036 0.002 PHE A 481 TRP 0.020 0.002 TRP A 269 HIS 0.016 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.49 ( 7310) covalent geometry : angle 0.74662 / 0.46 ( 9996) hydrogen bonds : bond 0.16785 / 11.30 ( 229) hydrogen bonds : angle 6.41861 / 4.19 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6480 (t80) cc_final: 0.6268 (t80) REVERT: A 107 LYS cc_start: 0.7410 (ptpp) cc_final: 0.7047 (ptmm) REVERT: A 349 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8340 (mtp85) REVERT: A 351 SER cc_start: 0.7788 (p) cc_final: 0.7370 (t) REVERT: A 436 LEU cc_start: 0.5855 (mt) cc_final: 0.5490 (mt) REVERT: C 151 ARG cc_start: 0.8566 (ttt90) cc_final: 0.7728 (ttp80) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.0707 time to fit residues: 16.7449 Evaluate side-chains 139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN A 177 ASN A 402 ASN C 6 HIS C 118 ASN C 137 ASN C 271 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.174904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154683 restraints weight = 11474.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.158522 restraints weight = 6890.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161108 restraints weight = 4548.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.162883 restraints weight = 3241.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.163947 restraints weight = 2467.773| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 7310 Z= 0.283 Angle : 0.779 10.140 9996 Z= 0.409 Chirality : 0.047 0.190 1226 Planarity : 0.005 0.056 1279 Dihedral : 7.964 77.820 1093 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 2.38 % Allowed : 15.58 % Favored : 82.03 % 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 are not related in a simple way. whole: -3.10 (0.26), residues: 1008 helix: -1.26 (0.24), residues: 435 sheet: -3.62 (0.44), residues: 107 loop : -2.39 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 93 TYR 0.021 0.002 TYR A 372 PHE 0.037 0.003 PHE C 260 TRP 0.031 0.004 TRP A 269 HIS 0.009 0.002 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 ( 7310) covalent geometry : angle 0.77895 / 0.41 ( 9996) hydrogen bonds : bond 0.04605 / 3.06 ( 229) hydrogen bonds : angle 5.70976 / 3.82 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7631 (ptpp) cc_final: 0.7266 (ptmm) REVERT: A 344 LEU cc_start: 0.7618 (tt) cc_final: 0.7337 (tt) REVERT: A 402 ASN cc_start: 0.5686 (m-40) cc_final: 0.5450 (p0) outliers start: 15 outliers final: 8 residues processed: 142 average time/residue: 0.0733 time to fit residues: 14.6192 Evaluate side-chains 138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 271 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [13, 48, 12, 52, 16, 61, 73, 72, 38, 49, 0] chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 52 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS A 524 HIS A 536 ASN C 5 HIS C 271 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.179186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157697 restraints weight = 11331.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.161997 restraints weight = 6509.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.164828 restraints weight = 4197.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.166744 restraints weight = 2938.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.168139 restraints weight = 2203.545| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.003 0.057 7310 Z= 0.138 Angle : 0.632 8.826 9996 Z= 0.332 Chirality : 0.042 0.176 1226 Planarity : 0.004 0.049 1279 Dihedral : 7.546 72.411 1093 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.02 % Allowed : 18.60 % Favored : 78.38 % 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 are not related in a simple way. whole: -2.78 (0.26), residues: 1008 helix: -0.98 (0.25), residues: 432 sheet: -3.26 (0.48), residues: 96 loop : -2.33 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 93 TYR 0.011 0.001 TYR A 432 PHE 0.026 0.002 PHE A 706 TRP 0.016 0.002 TRP A 269 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7310) covalent geometry : angle 0.63204 / 0.33 ( 9996) hydrogen bonds : bond 0.03331 / 2.23 ( 229) hydrogen bonds : angle 5.33387 / 3.50 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.5967 (t) cc_final: 0.4950 (p) REVERT: A 351 SER cc_start: 0.7882 (p) cc_final: 0.7319 (t) REVERT: A 402 ASN cc_start: 0.5608 (m-40) cc_final: 0.5195 (p0) REVERT: A 432 TYR cc_start: 0.7012 (m-80) cc_final: 0.6742 (m-80) REVERT: C 269 TRP cc_start: 0.7843 (t60) cc_final: 0.7568 (t60) outliers start: 19 outliers final: 10 residues processed: 141 average time/residue: 0.0649 time to fit residues: 13.3256 Evaluate side-chains 137 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [12, 57, 99, 60, 6, 2, 17, 52, 22, 14, 0] chunk 12 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157204 restraints weight = 11391.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.161054 restraints weight = 6734.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.163717 restraints weight = 4424.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.165491 restraints weight = 3121.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.166710 restraints weight = 2353.546| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7310 Z= 0.158 Angle : 0.634 8.690 9996 Z= 0.335 Chirality : 0.042 0.163 1226 Planarity : 0.004 0.046 1279 Dihedral : 7.462 69.857 1093 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 2.86 % Allowed : 20.67 % Favored : 76.47 % 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 are not related in a simple way. whole: -2.76 (0.26), residues: 1008 helix: -0.95 (0.25), residues: 438 sheet: -3.37 (0.47), residues: 96 loop : -2.32 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 93 TYR 0.012 0.001 TYR A 432 PHE 0.030 0.002 PHE A 286 TRP 0.017 0.002 TRP A 269 HIS 0.008 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7310) covalent geometry : angle 0.63410 / 0.33 ( 9996) hydrogen bonds : bond 0.03266 / 2.19 ( 229) hydrogen bonds : angle 5.36042 / 3.53 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.6117 (t) cc_final: 0.5110 (p) REVERT: A 257 VAL cc_start: 0.8224 (m) cc_final: 0.8017 (m) REVERT: A 402 ASN cc_start: 0.5624 (m-40) cc_final: 0.5288 (p0) REVERT: A 432 TYR cc_start: 0.7052 (m-80) cc_final: 0.6686 (m-80) outliers start: 18 outliers final: 15 residues processed: 136 average time/residue: 0.0721 time to fit residues: 14.0240 Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [54, 22, 57, 27, 20, 86, 74, 12, 19, 55, 72] chunk 54 optimal weight: 0.0980 chunk 22 optimal weight: 0.0010 chunk 57 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 0.0060 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 123 HIS C 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.180186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.159620 restraints weight = 11248.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.163771 restraints weight = 6500.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.166497 restraints weight = 4173.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.168365 restraints weight = 2898.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.169629 restraints weight = 2152.109| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7310 Z= 0.109 Angle : 0.594 8.798 9996 Z= 0.310 Chirality : 0.041 0.181 1226 Planarity : 0.004 0.043 1279 Dihedral : 7.282 67.719 1093 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 3.34 % Allowed : 20.83 % Favored : 75.83 % 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 are not related in a simple way. whole: -2.47 (0.27), residues: 1008 helix: -0.67 (0.25), residues: 431 sheet: -3.26 (0.48), residues: 90 loop : -2.20 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 93 TYR 0.007 0.001 TYR A 432 PHE 0.040 0.002 PHE A 286 TRP 0.009 0.001 TRP A 269 HIS 0.003 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7310) covalent geometry : angle 0.59398 / 0.31 ( 9996) hydrogen bonds : bond 0.02672 / 1.79 ( 229) hydrogen bonds : angle 5.14263 / 3.37 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.5975 (OUTLIER) cc_final: 0.4963 (p) REVERT: A 192 ASN cc_start: 0.6639 (m-40) cc_final: 0.6429 (m-40) REVERT: A 402 ASN cc_start: 0.5569 (m-40) cc_final: 0.5114 (p0) REVERT: A 432 TYR cc_start: 0.6980 (m-80) cc_final: 0.6553 (m-80) outliers start: 21 outliers final: 14 residues processed: 137 average time/residue: 0.0655 time to fit residues: 13.0051 Evaluate side-chains 140 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [21, 29, 74, 3, 51, 12, 97, 56, 23, 43, 75] chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 0.0570 chunk 74 optimal weight: 0.0010 chunk 3 optimal weight: 0.0770 chunk 51 optimal weight: 0.0020 chunk 12 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 overall best weight: 0.0308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS A 275 GLN C 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.181705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.160998 restraints weight = 11470.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.165205 restraints weight = 6637.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.167953 restraints weight = 4237.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.169793 restraints weight = 2941.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.171062 restraints weight = 2194.044| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7310 Z= 0.106 Angle : 0.584 9.136 9996 Z= 0.304 Chirality : 0.040 0.186 1226 Planarity : 0.004 0.041 1279 Dihedral : 7.060 64.600 1093 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 2.70 % Allowed : 21.94 % Favored : 75.36 % 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 are not related in a simple way. whole: -2.16 (0.27), residues: 1008 helix: -0.34 (0.26), residues: 418 sheet: -3.31 (0.48), residues: 90 loop : -2.02 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 93 TYR 0.006 0.001 TYR A 639 PHE 0.037 0.001 PHE A 286 TRP 0.008 0.001 TRP C 269 HIS 0.023 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 7310) covalent geometry : angle 0.58386 / 0.30 ( 9996) hydrogen bonds : bond 0.02457 / 1.65 ( 229) hydrogen bonds : angle 4.94342 / 3.24 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.5934 (t) cc_final: 0.4875 (p) REVERT: A 402 ASN cc_start: 0.5577 (m-40) cc_final: 0.5182 (p0) REVERT: C 117 ILE cc_start: 0.6312 (pt) cc_final: 0.6088 (pt) outliers start: 17 outliers final: 11 residues processed: 129 average time/residue: 0.0675 time to fit residues: 12.4624 Evaluate side-chains 136 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 6 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [31, 97, 16, 11, 76, 96, 69, 52, 29, 21, 79] chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS C 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.178103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157786 restraints weight = 11327.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.161774 restraints weight = 6701.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.164423 restraints weight = 4357.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.166221 restraints weight = 3049.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.167461 restraints weight = 2287.567| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7310 Z= 0.141 Angle : 0.615 9.599 9996 Z= 0.321 Chirality : 0.041 0.259 1226 Planarity : 0.004 0.042 1279 Dihedral : 7.015 63.592 1093 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 2.86 % Allowed : 22.42 % Favored : 74.72 % 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 are not related in a simple way. whole: -2.23 (0.27), residues: 1008 helix: -0.45 (0.26), residues: 423 sheet: -3.30 (0.49), residues: 91 loop : -2.04 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 93 TYR 0.015 0.001 TYR A 432 PHE 0.025 0.002 PHE A 286 TRP 0.015 0.002 TRP A 269 HIS 0.007 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7310) covalent geometry : angle 0.61477 / 0.32 ( 9996) hydrogen bonds : bond 0.02852 / 1.92 ( 229) hydrogen bonds : angle 4.94345 / 3.24 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ASN cc_start: 0.5663 (m-40) cc_final: 0.5229 (p0) REVERT: A 432 TYR cc_start: 0.6958 (m-80) cc_final: 0.6518 (m-80) outliers start: 18 outliers final: 16 residues processed: 131 average time/residue: 0.0702 time to fit residues: 13.2446 Evaluate side-chains 139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [92, 62, 36, 85, 38, 27, 8, 74, 7, 84, 12] chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 0.0050 chunk 38 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS C 137 ASN C 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.177694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.157515 restraints weight = 11410.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.161353 restraints weight = 6801.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163956 restraints weight = 4461.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.165726 restraints weight = 3160.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.166906 restraints weight = 2385.849| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7310 Z= 0.137 Angle : 0.625 9.815 9996 Z= 0.325 Chirality : 0.042 0.210 1226 Planarity : 0.004 0.043 1279 Dihedral : 7.048 62.643 1093 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 3.34 % Allowed : 22.42 % Favored : 74.24 % 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 are not related in a simple way. whole: -2.25 (0.27), residues: 1008 helix: -0.44 (0.26), residues: 422 sheet: -3.27 (0.50), residues: 91 loop : -2.07 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 93 TYR 0.013 0.001 TYR A 432 PHE 0.022 0.002 PHE A 286 TRP 0.018 0.002 TRP C 269 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7310) covalent geometry : angle 0.62476 / 0.32 ( 9996) hydrogen bonds : bond 0.02844 / 1.87 ( 229) hydrogen bonds : angle 4.95258 / 3.26 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7615 (tp) cc_final: 0.7415 (tp) REVERT: A 402 ASN cc_start: 0.5730 (m-40) cc_final: 0.5352 (p0) REVERT: A 432 TYR cc_start: 0.6931 (m-80) cc_final: 0.6548 (m-80) REVERT: C 269 TRP cc_start: 0.7694 (t60) cc_final: 0.7480 (t60) outliers start: 21 outliers final: 19 residues processed: 133 average time/residue: 0.0628 time to fit residues: 12.0664 Evaluate side-chains 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 271 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [0, 35, 66, 36, 2, 48, 30, 65, 93, 98, 23] chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 65 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS C 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.177772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157691 restraints weight = 11243.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.161556 restraints weight = 6724.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.164182 restraints weight = 4416.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165963 restraints weight = 3115.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.167224 restraints weight = 2341.880| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7310 Z= 0.128 Angle : 0.634 10.257 9996 Z= 0.329 Chirality : 0.043 0.411 1226 Planarity : 0.004 0.043 1279 Dihedral : 7.018 64.427 1093 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 3.02 % Allowed : 22.26 % Favored : 74.72 % 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 are not related in a simple way. whole: -2.27 (0.27), residues: 1008 helix: -0.47 (0.26), residues: 421 sheet: -3.24 (0.51), residues: 91 loop : -2.07 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 93 TYR 0.011 0.001 TYR A 432 PHE 0.020 0.001 PHE A 286 TRP 0.014 0.002 TRP C 269 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7310) covalent geometry : angle 0.63438 / 0.33 ( 9996) hydrogen bonds : bond 0.02790 / 1.84 ( 229) hydrogen bonds : angle 4.90363 / 3.23 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 402 ASN cc_start: 0.5913 (m-40) cc_final: 0.5502 (p0) REVERT: A 432 TYR cc_start: 0.6911 (m-80) cc_final: 0.6555 (m-80) outliers start: 19 outliers final: 16 residues processed: 131 average time/residue: 0.0642 time to fit residues: 12.1922 Evaluate side-chains 139 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [23, 99, 61, 16, 45, 49, 59, 39, 75, 62, 83] chunk 23 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.176088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156052 restraints weight = 11210.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.159981 restraints weight = 6634.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.162581 restraints weight = 4343.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.164370 restraints weight = 3063.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.165568 restraints weight = 2306.726| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7310 Z= 0.158 Angle : 0.674 11.087 9996 Z= 0.350 Chirality : 0.043 0.410 1226 Planarity : 0.004 0.042 1279 Dihedral : 7.070 65.889 1093 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 3.34 % Allowed : 22.42 % Favored : 74.24 % 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 are not related in a simple way. whole: -2.39 (0.27), residues: 1008 helix: -0.60 (0.26), residues: 428 sheet: -3.37 (0.49), residues: 92 loop : -2.10 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 93 TYR 0.017 0.001 TYR A 252 PHE 0.055 0.002 PHE C 28 TRP 0.014 0.002 TRP A 269 HIS 0.007 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 7310) covalent geometry : angle 0.67406 / 0.35 ( 9996) hydrogen bonds : bond 0.02944 / 1.94 ( 229) hydrogen bonds : angle 5.07812 / 3.34 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 402 ASN cc_start: 0.5664 (m-40) cc_final: 0.5273 (p0) REVERT: A 432 TYR cc_start: 0.6946 (m-80) cc_final: 0.6626 (m-80) outliers start: 21 outliers final: 19 residues processed: 132 average time/residue: 0.0675 time to fit residues: 12.8005 Evaluate side-chains 140 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [28, 34, 63, 85, 12, 18, 99, 33, 31, 6, 39] chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.178120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158069 restraints weight = 11309.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.161993 restraints weight = 6725.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.164586 restraints weight = 4409.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.166401 restraints weight = 3117.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.167578 restraints weight = 2341.309| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7310 Z= 0.119 Angle : 0.659 11.170 9996 Z= 0.338 Chirality : 0.042 0.408 1226 Planarity : 0.004 0.043 1279 Dihedral : 7.007 68.983 1093 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 2.54 % Allowed : 23.53 % Favored : 73.93 % Cbeta Deviations : 0.10 % 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 are not related in a simple way. whole: -2.26 (0.27), residues: 1008 helix: -0.52 (0.26), residues: 423 sheet: -2.96 (0.59), residues: 71 loop : -2.15 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 93 TYR 0.013 0.001 TYR A 252 PHE 0.051 0.002 PHE C 28 TRP 0.014 0.002 TRP C 269 HIS 0.015 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7310) covalent geometry : angle 0.65857 / 0.34 ( 9996) hydrogen bonds : bond 0.02684 / 1.76 ( 229) hydrogen bonds : angle 5.01398 / 3.29 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1335.80 seconds wall clock time: 23 minutes 32.10 seconds (1412.10 seconds total)