Starting phenix.real_space_refine on Thu Sep 18 00:06:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0o_39709/09_2025/8z0o_39709.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0o_39709/09_2025/8z0o_39709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z0o_39709/09_2025/8z0o_39709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0o_39709/09_2025/8z0o_39709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z0o_39709/09_2025/8z0o_39709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0o_39709/09_2025/8z0o_39709.map" } resolution = 3.2 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= 0.003 sd= 0.082 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 69 5.16 5 C 7984 2.51 5 N 2057 2.21 5 O 2180 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12296 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 6122 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 733} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 6122 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 733} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.96, per 1000 atoms: 0.24 Number of scatterers: 12296 At special positions: 0 Unit cell: (142.6, 76.36, 116.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 69 16.00 P 4 15.00 O 2180 8.00 N 2057 7.00 C 7984 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: 1.07 Conformation dependent library (CDL) restraints added in 548.6 milliseconds Enol-peptide restraints added in 1.4 microseconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 67.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 23 through 37 Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.195A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.552A pdb=" N PHE A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.812A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.519A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.545A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 489 No H-bonds generated for 'chain 'A' and resid 488 through 489' Processing helix chain 'A' and resid 491 through 494 removed outlier: 4.092A pdb=" N ALA A 494 " --> pdb=" O MET A 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 491 through 494' Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 528 through 554 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.520A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 620 through 646 removed outlier: 4.108A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 696 Processing helix chain 'A' and resid 696 through 706 Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.703A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 Processing helix chain 'A' and resid 764 through 819 Processing helix chain 'A' and resid 820 through 853 Proline residue: A 826 - end of helix Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.522A pdb=" N GLY A 857 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 136 through 163 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.663A pdb=" N PHE B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER B 215 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.829A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 357 through 374 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.561A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.751A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 528 through 554 Processing helix chain 'B' and resid 554 through 560 removed outlier: 4.432A pdb=" N TYR B 558 " --> pdb=" O TRP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 587 Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 619 through 646 removed outlier: 4.113A pdb=" N ASP B 623 " --> pdb=" O GLN B 619 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 681 Processing helix chain 'B' and resid 684 through 695 Processing helix chain 'B' and resid 696 through 706 Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.496A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.563A pdb=" N ASN B 736 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 819 Processing helix chain 'B' and resid 820 through 853 Proline residue: B 826 - end of helix Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.543A pdb=" N GLY B 857 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG B 858 " --> pdb=" O LEU B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 858' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 removed outlier: 8.201A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 326 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS A 514 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 408 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 516 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLY A 410 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASP A 518 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N LEU A 412 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL A 520 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N VAL A 414 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG A 522 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA3, first strand: chain 'B' and resid 177 through 180 removed outlier: 8.169A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 326 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 347 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS B 514 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 408 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 516 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY B 410 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASP B 518 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N LEU B 412 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL B 520 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N VAL B 414 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARG B 522 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337 806 hydrogen bonds defined for protein. 2376 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: 2.29 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.54: 12277 1.54 - 1.89: 342 1.89 - 2.25: 0 2.25 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 12620 Sorted by residual: bond pdb=" C GLY A 489 " pdb=" N MET A 491 " ideal model delta sigma weight residual 1.332 2.962 -1.630 1.40e-02 5.10e+03 1.35e+04 bond pdb=" O3A UDP B1001 " pdb=" PB UDP B1001 " ideal model delta sigma weight residual 1.584 1.640 -0.056 1.00e-02 1.00e+04 3.08e+01 bond pdb=" O3A UDP A1001 " pdb=" PB UDP A1001 " ideal model delta sigma weight residual 1.584 1.638 -0.054 1.00e-02 1.00e+04 2.93e+01 bond pdb=" O3B UDP B1001 " pdb=" PB UDP B1001 " ideal model delta sigma weight residual 1.494 1.658 -0.164 3.50e-02 8.16e+02 2.20e+01 bond pdb=" O3B UDP A1001 " pdb=" PB UDP A1001 " ideal model delta sigma weight residual 1.494 1.657 -0.163 3.50e-02 8.16e+02 2.16e+01 ... (remaining 12615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.08: 17111 8.08 - 16.16: 11 16.16 - 24.24: 2 24.24 - 32.32: 0 32.32 - 40.40: 1 Bond angle restraints: 17125 Sorted by residual: angle pdb=" O GLY A 489 " pdb=" C GLY A 489 " pdb=" N MET A 491 " ideal model delta sigma weight residual 122.70 82.30 40.40 1.30e+00 5.92e-01 9.66e+02 angle pdb=" O3A UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3B UDP A1001 " ideal model delta sigma weight residual 112.01 92.67 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" O3A UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3B UDP B1001 " ideal model delta sigma weight residual 112.01 93.41 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" O5' UDP A1001 " pdb=" PA UDP A1001 " pdb=" O3A UDP A1001 " ideal model delta sigma weight residual 104.35 92.73 11.62 1.00e+00 1.00e+00 1.35e+02 angle pdb=" O5' UDP B1001 " pdb=" PA UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 104.35 93.52 10.83 1.00e+00 1.00e+00 1.17e+02 ... (remaining 17120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 6792 22.41 - 44.82: 540 44.82 - 67.23: 40 67.23 - 89.64: 11 89.64 - 112.06: 1 Dihedral angle restraints: 7384 sinusoidal: 2943 harmonic: 4441 Sorted by residual: dihedral pdb=" CA GLY A 489 " pdb=" C GLY A 489 " pdb=" N MET A 491 " pdb=" CA MET A 491 " ideal model delta harmonic sigma weight residual 180.00 67.94 112.06 0 5.00e+00 4.00e-02 5.02e+02 dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 158.33 21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLN B 602 " pdb=" C GLN B 602 " pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1487 0.047 - 0.095: 331 0.095 - 0.142: 54 0.142 - 0.190: 3 0.190 - 0.237: 5 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CB ILE B 465 " pdb=" CA ILE B 465 " pdb=" CG1 ILE B 465 " pdb=" CG2 ILE B 465 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LEU A 645 " pdb=" N LEU A 645 " pdb=" C LEU A 645 " pdb=" CB LEU A 645 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 465 " pdb=" CA ILE A 465 " pdb=" CG1 ILE A 465 " pdb=" CG2 ILE A 465 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1877 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 489 " -0.168 2.00e-02 2.50e+03 2.23e-01 4.96e+02 pdb=" C GLY A 489 " 0.377 2.00e-02 2.50e+03 pdb=" O GLY A 489 " -0.159 2.00e-02 2.50e+03 pdb=" N MET A 491 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 644 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C GLY A 644 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 644 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 645 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 91 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO B 92 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " 0.039 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 302 2.70 - 3.25: 12148 3.25 - 3.80: 20027 3.80 - 4.35: 24214 4.35 - 4.90: 42724 Nonbonded interactions: 99415 Sorted by model distance: nonbonded pdb=" O2B UDP A1001 " pdb="MN MN A1002 " model vdw 2.152 2.320 nonbonded pdb=" O GLN B 619 " pdb=" NE2 GLN B 619 " model vdw 2.163 3.120 nonbonded pdb=" O HIS B 710 " pdb=" OG1 THR B 714 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLU B 197 " pdb=" NH1 ARG B 228 " model vdw 2.248 3.120 nonbonded pdb=" O GLY B 308 " pdb=" ND1 HIS B 331 " model vdw 2.249 3.120 ... (remaining 99410 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 23 through 39 or resid 91 through 121 or resid 123 through \ 124 or resid 128 through 131 or resid 133 through 649 or (resid 650 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 651 through 10 \ 02)) selection = (chain 'B' and (resid 23 through 147 or resid 149 through 161 or resid 163 throu \ gh 489 or resid 491 through 737 or resid 762 through 1002)) } 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 : 0.015 1.630 12620 Z= 1.062 Angle : 0.808 40.397 17125 Z= 0.530 Chirality : 0.041 0.237 1880 Planarity : 0.007 0.223 2152 Dihedral : 14.910 112.056 4528 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 2.30 % Allowed : 18.33 % Favored : 79.37 % 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: 1.29 (0.23), residues: 1496 helix: 1.95 (0.17), residues: 945 sheet: -0.67 (0.44), residues: 152 loop : -1.19 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 200 TYR 0.026 0.001 TYR A 207 PHE 0.040 0.002 PHE B 487 TRP 0.038 0.001 TRP A 202 HIS 0.004 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.01525 (12620) covalent geometry : angle 0.80822 (17125) hydrogen bonds : bond 0.10641 ( 806) hydrogen bonds : angle 5.92461 ( 2376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.464 Fit side-chains REVERT: A 300 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7685 (t) REVERT: A 403 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7436 (t-90) REVERT: A 418 PHE cc_start: 0.7423 (m-10) cc_final: 0.6109 (t80) REVERT: A 493 LEU cc_start: 0.5875 (mt) cc_final: 0.4647 (mp) REVERT: A 766 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7444 (mmmm) REVERT: B 300 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7738 (t) REVERT: B 524 ASP cc_start: 0.8971 (t70) cc_final: 0.8747 (t0) REVERT: B 651 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6947 (p-80) REVERT: B 657 TYR cc_start: 0.6989 (t80) cc_final: 0.6250 (t80) REVERT: B 715 PHE cc_start: 0.6992 (t80) cc_final: 0.6684 (t80) outliers start: 30 outliers final: 22 residues processed: 204 average time/residue: 0.1168 time to fit residues: 34.6788 Evaluate side-chains 189 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 716 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106610 restraints weight = 15688.035| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.70 r_work: 0.3168 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12620 Z= 0.122 Angle : 0.532 10.030 17125 Z= 0.276 Chirality : 0.038 0.140 1880 Planarity : 0.005 0.063 2152 Dihedral : 7.056 78.364 1761 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.99 % Allowed : 16.49 % Favored : 80.52 % 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: 1.40 (0.22), residues: 1498 helix: 2.09 (0.17), residues: 949 sheet: -0.84 (0.44), residues: 152 loop : -1.22 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.016 0.001 TYR B 207 PHE 0.038 0.001 PHE B 487 TRP 0.016 0.001 TRP A 202 HIS 0.003 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00261 (12620) covalent geometry : angle 0.53234 (17125) hydrogen bonds : bond 0.03856 ( 806) hydrogen bonds : angle 5.14185 ( 2376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.454 Fit side-chains REVERT: A 238 MET cc_start: 0.8902 (ttp) cc_final: 0.8680 (ptm) REVERT: A 418 PHE cc_start: 0.7462 (m-10) cc_final: 0.6242 (t80) REVERT: A 465 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 527 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7683 (m90) REVERT: A 622 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 766 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7593 (mmmm) REVERT: A 825 MET cc_start: 0.8648 (mmm) cc_final: 0.8439 (mmm) REVERT: B 322 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8735 (mm) REVERT: B 465 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7896 (tt) REVERT: B 524 ASP cc_start: 0.8933 (t70) cc_final: 0.8710 (t0) REVERT: B 651 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.6990 (p-80) REVERT: B 657 TYR cc_start: 0.7184 (t80) cc_final: 0.6408 (t80) REVERT: B 715 PHE cc_start: 0.7224 (t80) cc_final: 0.6916 (t80) REVERT: B 730 THR cc_start: 0.8800 (m) cc_final: 0.8539 (p) REVERT: B 825 MET cc_start: 0.8653 (mmm) cc_final: 0.8396 (mmm) outliers start: 39 outliers final: 18 residues processed: 212 average time/residue: 0.1047 time to fit residues: 33.3272 Evaluate side-chains 186 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 716 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 ASN A 411 GLN A 475 GLN A 619 GLN B 256 ASN B 402 ASN B 411 GLN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101442 restraints weight = 16394.351| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.63 r_work: 0.3089 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12620 Z= 0.193 Angle : 0.590 11.032 17125 Z= 0.304 Chirality : 0.041 0.171 1880 Planarity : 0.005 0.062 2152 Dihedral : 6.386 81.509 1740 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.52 % Allowed : 15.57 % Favored : 79.91 % 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: 1.23 (0.23), residues: 1498 helix: 2.00 (0.17), residues: 938 sheet: -1.29 (0.44), residues: 154 loop : -1.14 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 797 TYR 0.023 0.001 TYR A 207 PHE 0.022 0.002 PHE B 793 TRP 0.008 0.001 TRP A 202 HIS 0.004 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00447 (12620) covalent geometry : angle 0.59029 (17125) hydrogen bonds : bond 0.04225 ( 806) hydrogen bonds : angle 5.10228 ( 2376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8029 (tp30) cc_final: 0.7747 (tp30) REVERT: A 374 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8552 (tp40) REVERT: A 400 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 403 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: A 622 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 657 TYR cc_start: 0.7326 (t80) cc_final: 0.6565 (t80) REVERT: A 715 PHE cc_start: 0.7215 (t80) cc_final: 0.6989 (t80) REVERT: A 766 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7685 (mmmm) REVERT: B 37 ILE cc_start: 0.4885 (OUTLIER) cc_final: 0.4208 (mm) REVERT: B 148 PHE cc_start: 0.6302 (m-10) cc_final: 0.5949 (t80) REVERT: B 340 LYS cc_start: 0.7895 (mttt) cc_final: 0.7556 (mmmt) REVERT: B 400 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8455 (mm-30) REVERT: B 418 PHE cc_start: 0.7460 (m-10) cc_final: 0.6299 (t80) REVERT: B 465 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8190 (tt) REVERT: B 524 ASP cc_start: 0.8944 (t70) cc_final: 0.8709 (t0) REVERT: B 651 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7017 (p-80) REVERT: B 657 TYR cc_start: 0.7406 (t80) cc_final: 0.6608 (t80) REVERT: B 715 PHE cc_start: 0.7356 (t80) cc_final: 0.7006 (t80) REVERT: B 730 THR cc_start: 0.8831 (m) cc_final: 0.8562 (p) outliers start: 59 outliers final: 38 residues processed: 216 average time/residue: 0.1054 time to fit residues: 33.6459 Evaluate side-chains 208 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 786 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 89 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 619 GLN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104361 restraints weight = 15954.449| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.64 r_work: 0.3136 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12620 Z= 0.112 Angle : 0.503 9.809 17125 Z= 0.258 Chirality : 0.038 0.132 1880 Planarity : 0.004 0.060 2152 Dihedral : 6.050 84.990 1736 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.22 % Allowed : 17.94 % Favored : 78.83 % 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 aren not related in a simple way. whole: 1.42 (0.23), residues: 1498 helix: 2.16 (0.17), residues: 938 sheet: -1.11 (0.45), residues: 151 loop : -1.16 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 797 TYR 0.012 0.001 TYR A 207 PHE 0.038 0.001 PHE B 487 TRP 0.007 0.001 TRP A 539 HIS 0.002 0.000 HIS A 846 Details of bonding type rmsd covalent geometry : bond 0.00235 (12620) covalent geometry : angle 0.50312 (17125) hydrogen bonds : bond 0.03715 ( 806) hydrogen bonds : angle 4.98065 ( 2376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7981 (tp30) cc_final: 0.7712 (tp30) REVERT: A 400 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: A 415 ASP cc_start: 0.7916 (p0) cc_final: 0.7684 (t0) REVERT: A 527 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7721 (m90) REVERT: A 657 TYR cc_start: 0.7289 (t80) cc_final: 0.6515 (t80) REVERT: A 715 PHE cc_start: 0.7181 (t80) cc_final: 0.6958 (t80) REVERT: A 766 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7671 (mmmm) REVERT: A 797 ARG cc_start: 0.7889 (tmm-80) cc_final: 0.7678 (tmm-80) REVERT: B 37 ILE cc_start: 0.4951 (OUTLIER) cc_final: 0.4319 (mm) REVERT: B 148 PHE cc_start: 0.6234 (m-10) cc_final: 0.5787 (t80) REVERT: B 238 MET cc_start: 0.8874 (ttp) cc_final: 0.8652 (ptm) REVERT: B 340 LYS cc_start: 0.7912 (mttt) cc_final: 0.7554 (mmmt) REVERT: B 418 PHE cc_start: 0.7480 (m-10) cc_final: 0.6303 (t80) REVERT: B 465 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 480 GLU cc_start: 0.8322 (pm20) cc_final: 0.7947 (pm20) REVERT: B 524 ASP cc_start: 0.8903 (t70) cc_final: 0.8640 (t0) REVERT: B 657 TYR cc_start: 0.7315 (t80) cc_final: 0.6554 (t80) REVERT: B 667 MET cc_start: 0.7680 (tpp) cc_final: 0.6578 (tpp) REVERT: B 715 PHE cc_start: 0.7295 (t80) cc_final: 0.7014 (t80) outliers start: 42 outliers final: 28 residues processed: 199 average time/residue: 0.1129 time to fit residues: 32.9098 Evaluate side-chains 192 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 778 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102992 restraints weight = 16293.838| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.86 r_work: 0.3106 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12620 Z= 0.123 Angle : 0.500 9.852 17125 Z= 0.259 Chirality : 0.038 0.181 1880 Planarity : 0.004 0.056 2152 Dihedral : 5.886 85.569 1734 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.76 % Allowed : 17.56 % Favored : 78.68 % 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: 1.51 (0.23), residues: 1498 helix: 2.20 (0.17), residues: 940 sheet: -1.13 (0.46), residues: 153 loop : -1.03 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 797 TYR 0.019 0.001 TYR B 207 PHE 0.015 0.001 PHE B 545 TRP 0.005 0.001 TRP A 804 HIS 0.002 0.000 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00270 (12620) covalent geometry : angle 0.49979 (17125) hydrogen bonds : bond 0.03708 ( 806) hydrogen bonds : angle 4.94001 ( 2376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8004 (tp30) cc_final: 0.7725 (tp30) REVERT: A 196 GLU cc_start: 0.8426 (tt0) cc_final: 0.8002 (tp30) REVERT: A 400 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: A 527 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7726 (m90) REVERT: A 657 TYR cc_start: 0.7333 (t80) cc_final: 0.6553 (t80) REVERT: A 715 PHE cc_start: 0.7208 (t80) cc_final: 0.6979 (t80) REVERT: A 797 ARG cc_start: 0.7895 (tmm-80) cc_final: 0.7670 (tmm-80) REVERT: B 37 ILE cc_start: 0.5091 (OUTLIER) cc_final: 0.4450 (mm) REVERT: B 148 PHE cc_start: 0.6392 (m-10) cc_final: 0.5947 (t80) REVERT: B 238 MET cc_start: 0.8897 (ttp) cc_final: 0.8693 (ptm) REVERT: B 340 LYS cc_start: 0.7998 (mttt) cc_final: 0.7651 (mmmt) REVERT: B 418 PHE cc_start: 0.7421 (m-10) cc_final: 0.6345 (t80) REVERT: B 524 ASP cc_start: 0.8926 (t70) cc_final: 0.8645 (t0) REVERT: B 657 TYR cc_start: 0.7358 (t80) cc_final: 0.6618 (t80) REVERT: B 667 MET cc_start: 0.7769 (tpp) cc_final: 0.6555 (tpp) REVERT: B 715 PHE cc_start: 0.7324 (t80) cc_final: 0.7049 (t80) outliers start: 49 outliers final: 34 residues processed: 203 average time/residue: 0.1108 time to fit residues: 33.2737 Evaluate side-chains 197 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 778 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 327 HIS ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 ASN A 411 GLN A 606 GLN A 619 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN B 619 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.093839 restraints weight = 16434.152| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.63 r_work: 0.2992 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12620 Z= 0.242 Angle : 0.612 11.030 17125 Z= 0.316 Chirality : 0.042 0.212 1880 Planarity : 0.005 0.049 2152 Dihedral : 6.246 89.321 1732 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.21 % Allowed : 16.95 % Favored : 77.84 % 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 aren not related in a simple way. whole: 1.14 (0.23), residues: 1498 helix: 1.90 (0.17), residues: 937 sheet: -1.33 (0.45), residues: 153 loop : -1.08 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 797 TYR 0.022 0.002 TYR B 207 PHE 0.048 0.002 PHE B 487 TRP 0.009 0.001 TRP B 804 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00570 (12620) covalent geometry : angle 0.61188 (17125) hydrogen bonds : bond 0.04326 ( 806) hydrogen bonds : angle 5.16497 ( 2376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 167 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.4415 (OUTLIER) cc_final: 0.3989 (mm) REVERT: A 95 GLU cc_start: 0.8149 (tp30) cc_final: 0.7840 (tp30) REVERT: A 196 GLU cc_start: 0.8602 (tt0) cc_final: 0.8126 (tp30) REVERT: A 374 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8650 (tp40) REVERT: A 403 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7514 (t-90) REVERT: A 491 MET cc_start: 0.7352 (tmm) cc_final: 0.6529 (ppp) REVERT: A 657 TYR cc_start: 0.7532 (t80) cc_final: 0.6715 (t80) REVERT: A 715 PHE cc_start: 0.7248 (t80) cc_final: 0.7042 (t80) REVERT: A 797 ARG cc_start: 0.7919 (tmm-80) cc_final: 0.7616 (tmm-80) REVERT: B 148 PHE cc_start: 0.6587 (m-10) cc_final: 0.6196 (t80) REVERT: B 238 MET cc_start: 0.8924 (ttp) cc_final: 0.8690 (ptm) REVERT: B 295 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7956 (mm-40) REVERT: B 340 LYS cc_start: 0.8193 (mttt) cc_final: 0.7784 (mmmt) REVERT: B 651 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7046 (p-80) REVERT: B 657 TYR cc_start: 0.7451 (t80) cc_final: 0.7023 (t80) REVERT: B 667 MET cc_start: 0.8003 (tpp) cc_final: 0.6778 (tpp) REVERT: B 715 PHE cc_start: 0.7295 (t80) cc_final: 0.7001 (t80) outliers start: 68 outliers final: 44 residues processed: 215 average time/residue: 0.1060 time to fit residues: 33.9786 Evaluate side-chains 207 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 120 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099782 restraints weight = 16207.643| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.67 r_work: 0.3041 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12620 Z= 0.129 Angle : 0.524 9.938 17125 Z= 0.269 Chirality : 0.038 0.154 1880 Planarity : 0.004 0.044 2152 Dihedral : 6.101 88.779 1732 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.22 % Allowed : 19.48 % Favored : 77.30 % 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: 1.35 (0.23), residues: 1498 helix: 2.08 (0.17), residues: 938 sheet: -1.26 (0.45), residues: 153 loop : -1.04 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.017 0.001 TYR B 207 PHE 0.020 0.001 PHE B 545 TRP 0.006 0.001 TRP B 804 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00281 (12620) covalent geometry : angle 0.52376 (17125) hydrogen bonds : bond 0.03887 ( 806) hydrogen bonds : angle 5.05755 ( 2376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8133 (tp30) cc_final: 0.7804 (tp30) REVERT: A 196 GLU cc_start: 0.8554 (tt0) cc_final: 0.8055 (tp30) REVERT: A 480 GLU cc_start: 0.8046 (pm20) cc_final: 0.7741 (pm20) REVERT: A 491 MET cc_start: 0.7265 (tmm) cc_final: 0.6861 (ppp) REVERT: A 657 TYR cc_start: 0.7442 (t80) cc_final: 0.6621 (t80) REVERT: A 671 SER cc_start: 0.8549 (m) cc_final: 0.8320 (m) REVERT: A 715 PHE cc_start: 0.7218 (t80) cc_final: 0.7012 (t80) REVERT: A 797 ARG cc_start: 0.7848 (tmm-80) cc_final: 0.7597 (tmm-80) REVERT: B 115 ASP cc_start: 0.8587 (m-30) cc_final: 0.8235 (t0) REVERT: B 148 PHE cc_start: 0.6576 (m-10) cc_final: 0.6159 (t80) REVERT: B 295 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7991 (mm-40) REVERT: B 340 LYS cc_start: 0.8201 (mttt) cc_final: 0.7794 (mmmt) REVERT: B 657 TYR cc_start: 0.7423 (t80) cc_final: 0.6997 (t80) REVERT: B 667 MET cc_start: 0.7867 (tpp) cc_final: 0.6505 (tpp) REVERT: B 715 PHE cc_start: 0.7227 (t80) cc_final: 0.6954 (t80) REVERT: B 829 TYR cc_start: 0.8493 (m-10) cc_final: 0.8225 (m-10) outliers start: 42 outliers final: 37 residues processed: 198 average time/residue: 0.1153 time to fit residues: 33.4546 Evaluate side-chains 194 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN B 169 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095250 restraints weight = 16273.646| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.62 r_work: 0.3026 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12620 Z= 0.163 Angle : 0.559 11.207 17125 Z= 0.284 Chirality : 0.040 0.214 1880 Planarity : 0.004 0.041 2152 Dihedral : 6.146 89.933 1732 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.76 % Allowed : 18.63 % Favored : 77.61 % 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: 1.35 (0.23), residues: 1498 helix: 2.07 (0.17), residues: 940 sheet: -1.43 (0.45), residues: 157 loop : -0.94 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 856 TYR 0.019 0.001 TYR B 207 PHE 0.045 0.001 PHE B 487 TRP 0.006 0.001 TRP B 804 HIS 0.009 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00377 (12620) covalent geometry : angle 0.55889 (17125) hydrogen bonds : bond 0.03934 ( 806) hydrogen bonds : angle 5.07154 ( 2376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.4617 (OUTLIER) cc_final: 0.4201 (mm) REVERT: A 95 GLU cc_start: 0.8101 (tp30) cc_final: 0.7810 (tp30) REVERT: A 196 GLU cc_start: 0.8590 (tt0) cc_final: 0.8094 (tp30) REVERT: A 374 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8541 (tp40) REVERT: A 480 GLU cc_start: 0.8117 (pm20) cc_final: 0.7823 (pm20) REVERT: A 491 MET cc_start: 0.7422 (tmm) cc_final: 0.6555 (ppp) REVERT: A 657 TYR cc_start: 0.7447 (t80) cc_final: 0.6635 (t80) REVERT: A 668 MET cc_start: 0.8200 (mmm) cc_final: 0.7949 (mmt) REVERT: A 671 SER cc_start: 0.8575 (m) cc_final: 0.8356 (m) REVERT: A 715 PHE cc_start: 0.7243 (t80) cc_final: 0.7031 (t80) REVERT: B 115 ASP cc_start: 0.8622 (m-30) cc_final: 0.8275 (t0) REVERT: B 148 PHE cc_start: 0.6611 (m-10) cc_final: 0.6205 (t80) REVERT: B 295 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8015 (mm-40) REVERT: B 340 LYS cc_start: 0.8237 (mttt) cc_final: 0.7833 (mmmt) REVERT: B 651 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7054 (p-80) REVERT: B 657 TYR cc_start: 0.7445 (t80) cc_final: 0.7021 (t80) REVERT: B 667 MET cc_start: 0.7912 (tpp) cc_final: 0.6531 (tpp) REVERT: B 715 PHE cc_start: 0.7259 (t80) cc_final: 0.6985 (t80) REVERT: B 829 TYR cc_start: 0.8515 (m-10) cc_final: 0.8288 (m-10) outliers start: 49 outliers final: 37 residues processed: 198 average time/residue: 0.1136 time to fit residues: 33.0992 Evaluate side-chains 200 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN B 183 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098159 restraints weight = 16189.599| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.77 r_work: 0.3038 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12620 Z= 0.131 Angle : 0.524 10.073 17125 Z= 0.270 Chirality : 0.039 0.201 1880 Planarity : 0.004 0.040 2152 Dihedral : 6.073 88.840 1732 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.22 % Allowed : 19.33 % Favored : 77.45 % 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: 1.45 (0.23), residues: 1498 helix: 2.13 (0.17), residues: 940 sheet: -1.34 (0.45), residues: 155 loop : -0.89 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 772 TYR 0.016 0.001 TYR B 207 PHE 0.015 0.001 PHE A 329 TRP 0.006 0.001 TRP B 804 HIS 0.002 0.000 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00291 (12620) covalent geometry : angle 0.52420 (17125) hydrogen bonds : bond 0.03790 ( 806) hydrogen bonds : angle 5.00629 ( 2376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4377 (mm) REVERT: A 95 GLU cc_start: 0.8092 (tp30) cc_final: 0.7791 (tp30) REVERT: A 196 GLU cc_start: 0.8563 (tt0) cc_final: 0.8067 (tp30) REVERT: A 268 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: A 353 GLU cc_start: 0.8805 (tp30) cc_final: 0.7918 (tp30) REVERT: A 374 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8502 (tp40) REVERT: A 480 GLU cc_start: 0.8079 (pm20) cc_final: 0.7789 (pm20) REVERT: A 491 MET cc_start: 0.7401 (tmm) cc_final: 0.6470 (ppp) REVERT: A 657 TYR cc_start: 0.7440 (t80) cc_final: 0.6646 (t80) REVERT: A 667 MET cc_start: 0.7725 (mmm) cc_final: 0.7328 (tpp) REVERT: A 671 SER cc_start: 0.8569 (m) cc_final: 0.8350 (m) REVERT: A 715 PHE cc_start: 0.7240 (t80) cc_final: 0.7026 (t80) REVERT: A 779 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7213 (ttp80) REVERT: B 115 ASP cc_start: 0.8627 (m-30) cc_final: 0.8330 (t0) REVERT: B 148 PHE cc_start: 0.6629 (m-10) cc_final: 0.6238 (t80) REVERT: B 183 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7735 (p0) REVERT: B 295 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8046 (mm-40) REVERT: B 340 LYS cc_start: 0.8203 (mttt) cc_final: 0.7800 (mmmt) REVERT: B 569 MET cc_start: 0.8355 (mmp) cc_final: 0.8139 (mmp) REVERT: B 651 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7121 (p-80) REVERT: B 657 TYR cc_start: 0.7433 (t80) cc_final: 0.7004 (t80) REVERT: B 667 MET cc_start: 0.7898 (tpp) cc_final: 0.6475 (tpp) REVERT: B 715 PHE cc_start: 0.7264 (t80) cc_final: 0.6989 (t80) REVERT: B 829 TYR cc_start: 0.8503 (m-10) cc_final: 0.8244 (m-10) outliers start: 42 outliers final: 34 residues processed: 198 average time/residue: 0.1036 time to fit residues: 30.7116 Evaluate side-chains 197 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 9 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 133 optimal weight: 0.2980 chunk 145 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN A 647 ASN B 175 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099635 restraints weight = 16584.373| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.64 r_work: 0.3110 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12620 Z= 0.122 Angle : 0.519 9.281 17125 Z= 0.267 Chirality : 0.038 0.182 1880 Planarity : 0.004 0.040 2152 Dihedral : 6.040 87.914 1732 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.07 % Allowed : 19.63 % Favored : 77.30 % 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: 1.51 (0.23), residues: 1498 helix: 2.17 (0.17), residues: 940 sheet: -1.31 (0.45), residues: 155 loop : -0.83 (0.34), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 772 TYR 0.024 0.001 TYR B 207 PHE 0.022 0.001 PHE B 487 TRP 0.013 0.001 TRP B 184 HIS 0.002 0.000 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00264 (12620) covalent geometry : angle 0.51861 (17125) hydrogen bonds : bond 0.03715 ( 806) hydrogen bonds : angle 4.97093 ( 2376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4354 (mm) REVERT: A 95 GLU cc_start: 0.8130 (tp30) cc_final: 0.7850 (tp30) REVERT: A 196 GLU cc_start: 0.8566 (tt0) cc_final: 0.8138 (tp30) REVERT: A 268 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: A 353 GLU cc_start: 0.8760 (tp30) cc_final: 0.7926 (tp30) REVERT: A 374 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8554 (tp40) REVERT: A 491 MET cc_start: 0.7428 (tmm) cc_final: 0.6502 (ppp) REVERT: A 527 HIS cc_start: 0.8240 (p90) cc_final: 0.7831 (m90) REVERT: A 657 TYR cc_start: 0.7430 (t80) cc_final: 0.6638 (t80) REVERT: A 667 MET cc_start: 0.7725 (mmm) cc_final: 0.7339 (tpp) REVERT: A 671 SER cc_start: 0.8587 (m) cc_final: 0.8379 (m) REVERT: A 715 PHE cc_start: 0.7254 (t80) cc_final: 0.7043 (t80) REVERT: A 779 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7270 (ttp80) REVERT: B 115 ASP cc_start: 0.8629 (m-30) cc_final: 0.8306 (t0) REVERT: B 148 PHE cc_start: 0.6646 (m-10) cc_final: 0.6276 (t80) REVERT: B 196 GLU cc_start: 0.8467 (tt0) cc_final: 0.7924 (tp30) REVERT: B 295 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8087 (mm-40) REVERT: B 340 LYS cc_start: 0.8259 (mttt) cc_final: 0.7870 (mmmt) REVERT: B 651 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7172 (p-80) REVERT: B 657 TYR cc_start: 0.7476 (t80) cc_final: 0.7048 (t80) REVERT: B 667 MET cc_start: 0.7915 (tpp) cc_final: 0.6509 (tpp) REVERT: B 715 PHE cc_start: 0.7315 (t80) cc_final: 0.7041 (t80) REVERT: B 829 TYR cc_start: 0.8517 (m-10) cc_final: 0.8234 (m-10) outliers start: 40 outliers final: 32 residues processed: 193 average time/residue: 0.1115 time to fit residues: 31.6575 Evaluate side-chains 191 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 111 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN B 175 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099396 restraints weight = 16426.377| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.62 r_work: 0.3109 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12620 Z= 0.129 Angle : 0.523 10.262 17125 Z= 0.268 Chirality : 0.039 0.207 1880 Planarity : 0.004 0.040 2152 Dihedral : 6.020 87.380 1732 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.07 % Allowed : 19.63 % Favored : 77.30 % 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: 1.51 (0.23), residues: 1498 helix: 2.18 (0.17), residues: 939 sheet: -1.32 (0.46), residues: 153 loop : -0.86 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 772 TYR 0.023 0.001 TYR B 207 PHE 0.015 0.001 PHE B 601 TRP 0.010 0.001 TRP B 160 HIS 0.002 0.000 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00287 (12620) covalent geometry : angle 0.52275 (17125) hydrogen bonds : bond 0.03717 ( 806) hydrogen bonds : angle 4.96007 ( 2376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2478.41 seconds wall clock time: 43 minutes 32.66 seconds (2612.66 seconds total)