Starting phenix.real_space_refine on Wed Jul 30 13:49:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0o_39709/07_2025/8z0o_39709.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0o_39709/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0o_39709/07_2025/8z0o_39709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0o_39709/07_2025/8z0o_39709.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0o_39709/07_2025/8z0o_39709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0o_39709/07_2025/8z0o_39709.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.09, per 1000 atoms: 0.66 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.54 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: 5.02 Time building geometry restraints manager: 3.70 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 85 \ 9 or resid 1001 or resid 1002)) 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 859 or resid 1001 or resid \ 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: 1.790 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.260 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- 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 : 12.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (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 TRP 0.038 0.001 TRP A 202 HIS 0.004 0.001 HIS B 846 PHE 0.040 0.002 PHE B 487 TYR 0.026 0.001 TYR A 207 ARG 0.007 0.001 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.10641 ( 806) hydrogen bonds : angle 5.92461 ( 2376) covalent geometry : bond 0.01525 (12620) covalent geometry : angle 0.80822 (17125) *********************** 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 : 1.272 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: 0.2303 time to fit residues: 68.4372 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 : 1.317 ------------------------------------------------------------------------------- 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 128 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.0010 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.132520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104189 restraints weight = 15775.408| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.78 r_work: 0.3135 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12620 Z= 0.140 Angle : 0.543 10.275 17125 Z= 0.282 Chirality : 0.039 0.145 1880 Planarity : 0.005 0.063 2152 Dihedral : 7.130 79.122 1761 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 3.53 % Allowed : 16.03 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1498 helix: 2.03 (0.17), residues: 949 sheet: -0.90 (0.44), residues: 152 loop : -1.22 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 202 HIS 0.004 0.001 HIS A 331 PHE 0.039 0.001 PHE B 487 TYR 0.016 0.001 TYR A 207 ARG 0.006 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 806) hydrogen bonds : angle 5.15464 ( 2376) covalent geometry : bond 0.00312 (12620) covalent geometry : angle 0.54336 (17125) *********************** 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 228 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 238 MET cc_start: 0.8922 (ttp) cc_final: 0.8706 (ptm) REVERT: A 418 PHE cc_start: 0.7494 (m-10) cc_final: 0.6251 (t80) REVERT: A 465 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 622 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7739 (mp) REVERT: A 657 TYR cc_start: 0.7101 (t80) cc_final: 0.6389 (t80) REVERT: A 766 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7593 (mmmm) REVERT: A 825 MET cc_start: 0.8650 (mmm) cc_final: 0.8443 (mmm) REVERT: B 37 ILE cc_start: 0.4811 (OUTLIER) cc_final: 0.4204 (mm) REVERT: B 322 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8753 (mm) REVERT: B 340 LYS cc_start: 0.7679 (mttt) cc_final: 0.7431 (mmmt) REVERT: B 400 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8435 (mm-30) REVERT: B 465 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7935 (tt) REVERT: B 524 ASP cc_start: 0.8937 (t70) cc_final: 0.8727 (t0) REVERT: B 651 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7008 (p-80) REVERT: B 657 TYR cc_start: 0.7239 (t80) cc_final: 0.6451 (t80) REVERT: B 667 MET cc_start: 0.7426 (mmm) cc_final: 0.6999 (tpp) REVERT: B 715 PHE cc_start: 0.7249 (t80) cc_final: 0.6938 (t80) REVERT: B 730 THR cc_start: 0.8820 (m) cc_final: 0.8556 (p) REVERT: B 825 MET cc_start: 0.8659 (mmm) cc_final: 0.8405 (mmm) outliers start: 46 outliers final: 24 residues processed: 214 average time/residue: 0.2150 time to fit residues: 68.6682 Evaluate side-chains 194 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 400 GLU 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 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 37 ILE 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 426 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 651 HIS Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 2 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 475 GLN A 619 GLN B 256 ASN B 619 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102364 restraints weight = 16084.962| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.73 r_work: 0.3121 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 12620 Z= 0.146 Angle : 0.532 11.178 17125 Z= 0.274 Chirality : 0.039 0.171 1880 Planarity : 0.005 0.064 2152 Dihedral : 6.265 80.251 1741 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.60 % Allowed : 16.33 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1498 helix: 2.11 (0.17), residues: 948 sheet: -1.10 (0.44), residues: 152 loop : -1.15 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.003 0.001 HIS B 297 PHE 0.018 0.001 PHE A 545 TYR 0.016 0.001 TYR A 207 ARG 0.005 0.000 ARG B 797 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 806) hydrogen bonds : angle 5.01949 ( 2376) covalent geometry : bond 0.00335 (12620) covalent geometry : angle 0.53166 (17125) *********************** 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 222 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 403 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7218 (t-90) REVERT: A 418 PHE cc_start: 0.7643 (m-10) cc_final: 0.6352 (t80) REVERT: A 465 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8136 (tt) REVERT: A 527 HIS cc_start: 0.8207 (p90) cc_final: 0.7664 (m90) REVERT: A 622 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 657 TYR cc_start: 0.7200 (t80) cc_final: 0.6473 (t80) REVERT: A 715 PHE cc_start: 0.7136 (t80) cc_final: 0.6916 (t80) REVERT: A 766 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7643 (mmmm) REVERT: B 37 ILE cc_start: 0.4918 (OUTLIER) cc_final: 0.4292 (mm) REVERT: B 148 PHE cc_start: 0.6158 (m-10) cc_final: 0.5858 (t80) REVERT: B 340 LYS cc_start: 0.7781 (mttt) cc_final: 0.7438 (mmmt) REVERT: B 418 PHE cc_start: 0.7345 (m-10) cc_final: 0.6154 (t80) REVERT: B 465 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8043 (tt) REVERT: B 524 ASP cc_start: 0.8961 (t70) cc_final: 0.8707 (t0) REVERT: B 651 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.6964 (p-80) REVERT: B 657 TYR cc_start: 0.7301 (t80) cc_final: 0.6500 (t80) REVERT: B 715 PHE cc_start: 0.7247 (t80) cc_final: 0.6967 (t80) REVERT: B 730 THR cc_start: 0.8823 (m) cc_final: 0.8539 (p) outliers start: 47 outliers final: 30 residues processed: 206 average time/residue: 0.2227 time to fit residues: 68.2994 Evaluate side-chains 199 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 357 SER 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 465 ILE Chi-restraints excluded: chain A residue 520 VAL 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 690 VAL 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 177 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 327 HIS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 357 SER 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 564 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 651 HIS 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 769 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 0.0270 chunk 4 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 475 GLN B 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103641 restraints weight = 16092.073| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.75 r_work: 0.3155 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12620 Z= 0.117 Angle : 0.493 9.296 17125 Z= 0.254 Chirality : 0.037 0.132 1880 Planarity : 0.004 0.058 2152 Dihedral : 6.100 82.355 1741 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.60 % Allowed : 17.10 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.23), residues: 1498 helix: 2.23 (0.17), residues: 939 sheet: -1.16 (0.44), residues: 154 loop : -1.07 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.003 0.001 HIS A 846 PHE 0.021 0.001 PHE B 487 TYR 0.018 0.001 TYR B 581 ARG 0.006 0.000 ARG B 797 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 806) hydrogen bonds : angle 4.91609 ( 2376) covalent geometry : bond 0.00252 (12620) covalent geometry : angle 0.49311 (17125) *********************** 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 222 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7981 (tp30) cc_final: 0.7711 (tp30) REVERT: A 400 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 415 ASP cc_start: 0.7922 (p0) cc_final: 0.7670 (t0) REVERT: A 527 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7729 (m90) REVERT: A 657 TYR cc_start: 0.7254 (t80) cc_final: 0.6507 (t80) REVERT: A 766 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7677 (mmmm) REVERT: B 148 PHE cc_start: 0.6225 (m-10) cc_final: 0.5885 (t80) REVERT: B 238 MET cc_start: 0.8878 (ttp) cc_final: 0.8654 (ptm) REVERT: B 340 LYS cc_start: 0.7878 (mttt) cc_final: 0.7526 (mmmt) REVERT: B 480 GLU cc_start: 0.8313 (pm20) cc_final: 0.7933 (pm20) REVERT: B 524 ASP cc_start: 0.8925 (t70) cc_final: 0.8681 (t0) REVERT: B 657 TYR cc_start: 0.7335 (t80) cc_final: 0.6558 (t80) REVERT: B 715 PHE cc_start: 0.7301 (t80) cc_final: 0.7032 (t80) outliers start: 47 outliers final: 32 residues processed: 204 average time/residue: 0.2317 time to fit residues: 69.6630 Evaluate side-chains 194 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 388 THR 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 615 SER Chi-restraints excluded: chain A residue 628 ILE 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 193 MET Chi-restraints excluded: chain B residue 204 THR 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 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 693 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 733 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 619 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107076 restraints weight = 16127.512| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.88 r_work: 0.3135 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12620 Z= 0.118 Angle : 0.497 9.472 17125 Z= 0.255 Chirality : 0.038 0.170 1880 Planarity : 0.004 0.050 2152 Dihedral : 5.792 82.737 1735 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.68 % Allowed : 17.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1498 helix: 2.25 (0.17), residues: 940 sheet: -1.12 (0.45), residues: 154 loop : -0.96 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 804 HIS 0.002 0.000 HIS B 846 PHE 0.018 0.001 PHE A 192 TYR 0.016 0.001 TYR B 581 ARG 0.003 0.000 ARG A 797 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 806) hydrogen bonds : angle 4.89943 ( 2376) covalent geometry : bond 0.00256 (12620) covalent geometry : angle 0.49658 (17125) *********************** 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 220 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7976 (tp30) cc_final: 0.7700 (tp30) REVERT: A 400 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: A 403 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7315 (t-90) REVERT: A 527 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7731 (m90) REVERT: A 657 TYR cc_start: 0.7265 (t80) cc_final: 0.6513 (t80) REVERT: A 766 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7672 (mmmm) REVERT: B 37 ILE cc_start: 0.5035 (OUTLIER) cc_final: 0.4424 (mm) REVERT: B 115 ASP cc_start: 0.8282 (m-30) cc_final: 0.7793 (t0) REVERT: B 148 PHE cc_start: 0.6245 (m-10) cc_final: 0.5779 (t80) REVERT: B 238 MET cc_start: 0.8874 (ttp) cc_final: 0.8671 (ptm) REVERT: B 340 LYS cc_start: 0.7911 (mttt) cc_final: 0.7553 (mmmt) REVERT: B 480 GLU cc_start: 0.8271 (pm20) cc_final: 0.8069 (pm20) REVERT: B 524 ASP cc_start: 0.8931 (t70) cc_final: 0.8675 (t0) REVERT: B 657 TYR cc_start: 0.7375 (t80) cc_final: 0.6618 (t80) REVERT: B 715 PHE cc_start: 0.7305 (t80) cc_final: 0.7047 (t80) outliers start: 48 outliers final: 32 residues processed: 207 average time/residue: 0.2239 time to fit residues: 68.5582 Evaluate side-chains 202 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 137 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 34 optimal weight: 0.0370 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- 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 619 GLN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 411 GLN B 490 ASN B 619 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096172 restraints weight = 16477.870| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.65 r_work: 0.3027 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12620 Z= 0.198 Angle : 0.579 9.399 17125 Z= 0.299 Chirality : 0.041 0.201 1880 Planarity : 0.005 0.048 2152 Dihedral : 6.118 86.434 1735 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.14 % Allowed : 16.56 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1498 helix: 2.00 (0.17), residues: 940 sheet: -1.41 (0.44), residues: 155 loop : -0.96 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 539 HIS 0.004 0.001 HIS A 514 PHE 0.056 0.002 PHE B 487 TYR 0.022 0.002 TYR B 207 ARG 0.004 0.001 ARG A 797 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 806) hydrogen bonds : angle 5.07792 ( 2376) covalent geometry : bond 0.00461 (12620) covalent geometry : angle 0.57948 (17125) *********************** 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 234 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.4251 (mm) REVERT: A 95 GLU cc_start: 0.8133 (tp30) cc_final: 0.7832 (tp30) REVERT: A 196 GLU cc_start: 0.8543 (tt0) cc_final: 0.8119 (tp30) REVERT: A 374 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8677 (tp40) REVERT: A 403 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7486 (t-90) REVERT: A 657 TYR cc_start: 0.7427 (t80) cc_final: 0.6632 (t80) REVERT: A 715 PHE cc_start: 0.7286 (t80) cc_final: 0.7077 (t80) REVERT: B 113 TYR cc_start: 0.8178 (m-80) cc_final: 0.7582 (m-80) REVERT: B 148 PHE cc_start: 0.6521 (m-10) cc_final: 0.6154 (t80) REVERT: B 238 MET cc_start: 0.8907 (ttp) cc_final: 0.8682 (ptm) REVERT: B 295 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8027 (mm-40) REVERT: B 340 LYS cc_start: 0.8156 (mttt) cc_final: 0.7774 (mmmt) REVERT: B 651 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.6995 (p-80) REVERT: B 657 TYR cc_start: 0.7355 (t80) cc_final: 0.6616 (t80) REVERT: B 667 MET cc_start: 0.7974 (tpp) cc_final: 0.6975 (tpp) REVERT: B 715 PHE cc_start: 0.7299 (t80) cc_final: 0.7024 (t80) REVERT: B 829 TYR cc_start: 0.8528 (m-10) cc_final: 0.8322 (m-10) outliers start: 67 outliers final: 42 residues processed: 217 average time/residue: 0.2704 time to fit residues: 87.7496 Evaluate side-chains 201 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 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 564 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 620 THR 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 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 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 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 769 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** A 606 GLN B 327 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099667 restraints weight = 16194.190| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.60 r_work: 0.3062 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12620 Z= 0.133 Angle : 0.517 9.331 17125 Z= 0.267 Chirality : 0.039 0.146 1880 Planarity : 0.004 0.047 2152 Dihedral : 6.007 89.515 1733 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.53 % Allowed : 18.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.23), residues: 1498 helix: 2.11 (0.17), residues: 940 sheet: -1.19 (0.46), residues: 151 loop : -1.00 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.011 0.001 HIS A 327 PHE 0.018 0.001 PHE A 487 TYR 0.017 0.001 TYR B 207 ARG 0.003 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 806) hydrogen bonds : angle 5.01793 ( 2376) covalent geometry : bond 0.00295 (12620) covalent geometry : angle 0.51741 (17125) *********************** 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 216 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8116 (tp30) cc_final: 0.7821 (tp30) REVERT: A 196 GLU cc_start: 0.8523 (tt0) cc_final: 0.8045 (tp30) REVERT: A 295 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8070 (mm-40) REVERT: A 353 GLU cc_start: 0.8805 (tp30) cc_final: 0.7847 (tp30) REVERT: A 374 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8534 (tp40) REVERT: A 480 GLU cc_start: 0.8041 (pm20) cc_final: 0.7745 (pm20) REVERT: A 491 MET cc_start: 0.7544 (tmm) cc_final: 0.6730 (ppp) REVERT: A 527 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7789 (m90) REVERT: A 657 TYR cc_start: 0.7408 (t80) cc_final: 0.6590 (t80) REVERT: A 715 PHE cc_start: 0.7253 (t80) cc_final: 0.7047 (t80) REVERT: A 829 TYR cc_start: 0.8491 (m-10) cc_final: 0.8222 (m-10) REVERT: B 115 ASP cc_start: 0.8439 (m-30) cc_final: 0.8039 (t0) REVERT: B 148 PHE cc_start: 0.6567 (m-10) cc_final: 0.6155 (t80) REVERT: B 295 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7989 (mm-40) REVERT: B 340 LYS cc_start: 0.8149 (mttt) cc_final: 0.7722 (mmmt) REVERT: B 657 TYR cc_start: 0.7365 (t80) cc_final: 0.6942 (t80) REVERT: B 667 MET cc_start: 0.7835 (tpp) cc_final: 0.6759 (tpp) REVERT: B 715 PHE cc_start: 0.7260 (t80) cc_final: 0.6995 (t80) REVERT: B 829 TYR cc_start: 0.8507 (m-10) cc_final: 0.8291 (m-10) outliers start: 46 outliers final: 35 residues processed: 203 average time/residue: 0.3256 time to fit residues: 100.8233 Evaluate side-chains 196 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 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 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 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 193 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 215 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 183 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099815 restraints weight = 16176.181| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.64 r_work: 0.3076 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12620 Z= 0.122 Angle : 0.531 11.147 17125 Z= 0.270 Chirality : 0.039 0.248 1880 Planarity : 0.004 0.043 2152 Dihedral : 5.976 89.471 1733 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.53 % Allowed : 18.94 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1498 helix: 2.18 (0.17), residues: 940 sheet: -1.36 (0.46), residues: 151 loop : -0.94 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.004 0.001 HIS A 327 PHE 0.039 0.001 PHE B 487 TYR 0.017 0.001 TYR B 207 ARG 0.020 0.000 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 806) hydrogen bonds : angle 4.99706 ( 2376) covalent geometry : bond 0.00265 (12620) covalent geometry : angle 0.53087 (17125) *********************** 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 209 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8093 (tp30) cc_final: 0.7777 (tp30) REVERT: A 196 GLU cc_start: 0.8546 (tt0) cc_final: 0.8051 (tp30) REVERT: A 295 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8038 (mm-40) REVERT: A 353 GLU cc_start: 0.8782 (tp30) cc_final: 0.7948 (tp30) REVERT: A 374 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8515 (tp40) REVERT: A 480 GLU cc_start: 0.8006 (pm20) cc_final: 0.7712 (pm20) REVERT: A 491 MET cc_start: 0.7507 (tmm) cc_final: 0.6633 (ppp) REVERT: A 527 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7785 (m90) REVERT: A 657 TYR cc_start: 0.7390 (t80) cc_final: 0.6574 (t80) REVERT: A 715 PHE cc_start: 0.7219 (t80) cc_final: 0.7016 (t80) REVERT: B 115 ASP cc_start: 0.8445 (m-30) cc_final: 0.8060 (t0) REVERT: B 148 PHE cc_start: 0.6555 (m-10) cc_final: 0.6163 (t80) REVERT: B 295 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7985 (mm-40) REVERT: B 340 LYS cc_start: 0.8155 (mttt) cc_final: 0.7755 (mmmt) REVERT: B 651 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.6976 (p-80) REVERT: B 657 TYR cc_start: 0.7353 (t80) cc_final: 0.6935 (t80) REVERT: B 667 MET cc_start: 0.7839 (tpp) cc_final: 0.6711 (tpp) REVERT: B 715 PHE cc_start: 0.7238 (t80) cc_final: 0.6987 (t80) REVERT: B 829 TYR cc_start: 0.8482 (m-10) cc_final: 0.8180 (m-10) outliers start: 46 outliers final: 32 residues processed: 196 average time/residue: 0.2300 time to fit residues: 67.0906 Evaluate side-chains 189 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 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 215 SER 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 372 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.098815 restraints weight = 16543.288| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.66 r_work: 0.3100 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12620 Z= 0.154 Angle : 0.545 9.580 17125 Z= 0.280 Chirality : 0.039 0.204 1880 Planarity : 0.004 0.041 2152 Dihedral : 5.994 88.258 1733 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.14 % Allowed : 19.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1498 helix: 2.17 (0.17), residues: 940 sheet: -1.35 (0.45), residues: 155 loop : -0.92 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 846 PHE 0.017 0.001 PHE A 487 TYR 0.026 0.001 TYR B 207 ARG 0.005 0.000 ARG A 856 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 806) hydrogen bonds : angle 4.99084 ( 2376) covalent geometry : bond 0.00353 (12620) covalent geometry : angle 0.54477 (17125) *********************** 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 203 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8129 (tp30) cc_final: 0.7864 (tp30) REVERT: A 196 GLU cc_start: 0.8570 (tt0) cc_final: 0.8104 (tp30) REVERT: A 295 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8078 (mm-40) REVERT: A 374 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8669 (tp40) REVERT: A 480 GLU cc_start: 0.8150 (pm20) cc_final: 0.7853 (pm20) REVERT: A 527 HIS cc_start: 0.8257 (p90) cc_final: 0.7836 (m90) REVERT: A 657 TYR cc_start: 0.7478 (t80) cc_final: 0.6656 (t80) REVERT: A 715 PHE cc_start: 0.7298 (t80) cc_final: 0.7096 (t80) REVERT: B 115 ASP cc_start: 0.8487 (m-30) cc_final: 0.8139 (t0) REVERT: B 148 PHE cc_start: 0.6676 (m-10) cc_final: 0.6297 (t80) REVERT: B 295 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8076 (mm-40) REVERT: B 340 LYS cc_start: 0.8249 (mttt) cc_final: 0.7873 (mmmt) REVERT: B 382 ASP cc_start: 0.8697 (m-30) cc_final: 0.8462 (m-30) REVERT: B 651 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7004 (p-80) REVERT: B 657 TYR cc_start: 0.7437 (t80) cc_final: 0.7018 (t80) REVERT: B 667 MET cc_start: 0.8000 (tpp) cc_final: 0.6890 (tpp) REVERT: B 715 PHE cc_start: 0.7319 (t80) cc_final: 0.7055 (t80) REVERT: B 829 TYR cc_start: 0.8523 (m-10) cc_final: 0.8297 (m-10) outliers start: 41 outliers final: 35 residues processed: 192 average time/residue: 0.2263 time to fit residues: 64.1892 Evaluate side-chains 195 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 528 ASP Chi-restraints excluded: chain A residue 564 THR 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 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 215 SER 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 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 372 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101478 restraints weight = 16381.502| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.65 r_work: 0.3135 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3084 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= 0.117 Angle : 0.512 9.205 17125 Z= 0.266 Chirality : 0.038 0.164 1880 Planarity : 0.004 0.040 2152 Dihedral : 5.935 85.999 1733 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.61 % Allowed : 20.55 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1498 helix: 2.24 (0.17), residues: 940 sheet: -1.24 (0.45), residues: 155 loop : -0.83 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 552 HIS 0.002 0.000 HIS B 846 PHE 0.018 0.001 PHE B 487 TYR 0.020 0.001 TYR B 207 ARG 0.006 0.000 ARG B 772 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 806) hydrogen bonds : angle 4.92083 ( 2376) covalent geometry : bond 0.00251 (12620) covalent geometry : angle 0.51199 (17125) ********************** 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 199 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8104 (tp30) cc_final: 0.7845 (tp30) REVERT: A 115 ASP cc_start: 0.8636 (m-30) cc_final: 0.8180 (t0) REVERT: A 196 GLU cc_start: 0.8584 (tt0) cc_final: 0.8108 (tp30) REVERT: A 295 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8078 (mm-40) REVERT: A 353 GLU cc_start: 0.8765 (tp30) cc_final: 0.7930 (tp30) REVERT: A 374 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8524 (tp40) REVERT: A 527 HIS cc_start: 0.8202 (p90) cc_final: 0.7786 (m90) REVERT: A 657 TYR cc_start: 0.7442 (t80) cc_final: 0.6638 (t80) REVERT: A 715 PHE cc_start: 0.7238 (t80) cc_final: 0.7035 (t80) REVERT: A 779 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7260 (ttp80) REVERT: A 785 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.7014 (ttp80) REVERT: B 115 ASP cc_start: 0.8501 (m-30) cc_final: 0.8026 (t0) REVERT: B 148 PHE cc_start: 0.6655 (m-10) cc_final: 0.6295 (t80) REVERT: B 196 GLU cc_start: 0.8378 (tt0) cc_final: 0.7915 (tp30) REVERT: B 295 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8091 (mm-40) REVERT: B 340 LYS cc_start: 0.8268 (mttt) cc_final: 0.7873 (mmmt) REVERT: B 382 ASP cc_start: 0.8665 (m-30) cc_final: 0.8402 (m-30) REVERT: B 651 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.7015 (p-80) REVERT: B 657 TYR cc_start: 0.7424 (t80) cc_final: 0.7002 (t80) REVERT: B 667 MET cc_start: 0.7901 (tpp) cc_final: 0.6735 (tpp) REVERT: B 715 PHE cc_start: 0.7288 (t80) cc_final: 0.7048 (t80) outliers start: 34 outliers final: 31 residues processed: 192 average time/residue: 0.2566 time to fit residues: 71.2689 Evaluate side-chains 190 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 388 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 ASP 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 215 SER Chi-restraints excluded: chain B residue 343 LEU 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 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 725 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 84 optimal weight: 0.0570 chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- 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 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101436 restraints weight = 16348.032| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.64 r_work: 0.3133 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3189 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= 0.121 Angle : 0.514 8.655 17125 Z= 0.266 Chirality : 0.038 0.167 1880 Planarity : 0.004 0.041 2152 Dihedral : 5.881 85.583 1733 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.53 % Allowed : 20.32 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1498 helix: 2.26 (0.17), residues: 939 sheet: -1.34 (0.45), residues: 153 loop : -0.82 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 552 HIS 0.002 0.000 HIS B 846 PHE 0.017 0.001 PHE A 487 TYR 0.015 0.001 TYR A 829 ARG 0.006 0.000 ARG B 772 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 806) hydrogen bonds : angle 4.90422 ( 2376) covalent geometry : bond 0.00265 (12620) covalent geometry : angle 0.51377 (17125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5214.75 seconds wall clock time: 91 minutes 56.04 seconds (5516.04 seconds total)