Starting phenix.real_space_refine on Wed May 14 19:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y48_38910/05_2025/8y48_38910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y48_38910/05_2025/8y48_38910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y48_38910/05_2025/8y48_38910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y48_38910/05_2025/8y48_38910.map" model { file = "/net/cci-nas-00/data/ceres_data/8y48_38910/05_2025/8y48_38910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y48_38910/05_2025/8y48_38910.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 7585 2.51 5 N 2112 2.21 5 O 2325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12051 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4018 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 12, 'TYR:plan': 11, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 270 Chain: "B" Number of atoms: 4018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4018 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 12, 'TYR:plan': 11, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 270 Chain: "C" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4015 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 12, 'TYR:plan': 11, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 270 Time building chain proxies: 7.46, per 1000 atoms: 0.62 Number of scatterers: 12051 At special positions: 0 Unit cell: (90.63, 89.775, 183.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 2325 8.00 N 2112 7.00 C 7585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 362 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 24 sheets defined 15.9% alpha, 28.5% 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 149 through 154 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 366 through 379 Processing helix chain 'A' and resid 456 through 498 removed outlier: 3.807A pdb=" N GLN A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.806A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.720A pdb=" N SER A 652 " --> pdb=" O LYS A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 366 through 379 Processing helix chain 'B' and resid 456 through 498 removed outlier: 3.807A pdb=" N GLN B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.806A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 644 through 652 removed outlier: 3.720A pdb=" N SER B 652 " --> pdb=" O LYS B 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 366 through 379 Processing helix chain 'C' and resid 456 through 498 removed outlier: 3.807A pdb=" N GLN C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 510 removed outlier: 3.807A pdb=" N VAL C 505 " --> pdb=" O ASN C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 644 through 652 removed outlier: 3.720A pdb=" N SER C 652 " --> pdb=" O LYS C 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 515 through 519 removed outlier: 3.544A pdb=" N SER B 619 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 323 removed outlier: 5.384A pdb=" N LEU A 319 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS A 102 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS A 321 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 95 " --> pdb=" O MET A 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 349 removed outlier: 3.715A pdb=" N ALA A 348 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 327 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 94 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 95 " --> pdb=" O MET A 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.516A pdb=" N SER A 199 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS A 222 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS A 111 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA A 306 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 305 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 293 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 538 Processing sheet with id=AA8, first strand: chain 'A' and resid 593 through 597 Processing sheet with id=AA9, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.943A pdb=" N SER A 619 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 75 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 515 through 519 removed outlier: 3.553A pdb=" N LYS B 517 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 619 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 318 through 323 removed outlier: 5.383A pdb=" N LEU B 319 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS B 102 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS B 321 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 95 " --> pdb=" O MET B 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 344 through 349 removed outlier: 3.714A pdb=" N ALA B 348 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 327 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B 94 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 95 " --> pdb=" O MET B 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 186 removed outlier: 3.515A pdb=" N SER B 199 " --> pdb=" O CYS B 222 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS B 222 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS B 111 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA B 306 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 305 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 293 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AB7, first strand: chain 'B' and resid 536 through 538 Processing sheet with id=AB8, first strand: chain 'B' and resid 593 through 597 Processing sheet with id=AB9, first strand: chain 'C' and resid 318 through 323 removed outlier: 5.383A pdb=" N LEU C 319 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS C 102 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS C 321 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 95 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 344 through 349 removed outlier: 3.715A pdb=" N ALA C 348 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 327 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN C 94 " --> pdb=" O GLN C 328 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 95 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'C' and resid 185 through 186 removed outlier: 3.516A pdb=" N SER C 199 " --> pdb=" O CYS C 222 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS C 222 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS C 111 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA C 306 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP C 305 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 293 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AC5, first strand: chain 'C' and resid 536 through 538 Processing sheet with id=AC6, first strand: chain 'C' and resid 593 through 597 500 hydrogen bonds defined for protein. 1332 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: 4.10 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4062 1.35 - 1.46: 2795 1.46 - 1.58: 5400 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 12291 Sorted by residual: bond pdb=" N ILE A 523 " pdb=" CA ILE A 523 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" CA SER B 524 " pdb=" CB SER B 524 " ideal model delta sigma weight residual 1.530 1.482 0.049 1.50e-02 4.44e+03 1.07e+01 bond pdb=" CA SER B 515 " pdb=" CB SER B 515 " ideal model delta sigma weight residual 1.533 1.486 0.047 1.66e-02 3.63e+03 8.10e+00 bond pdb=" N ILE A 596 " pdb=" CA ILE A 596 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.22e-02 6.72e+03 8.00e+00 bond pdb=" N VAL C 525 " pdb=" CA VAL C 525 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.26e-02 6.30e+03 7.94e+00 ... (remaining 12286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 16584 1.68 - 3.37: 256 3.37 - 5.05: 32 5.05 - 6.73: 0 6.73 - 8.42: 3 Bond angle restraints: 16875 Sorted by residual: angle pdb=" CA ILE A 523 " pdb=" C ILE A 523 " pdb=" O ILE A 523 " ideal model delta sigma weight residual 121.63 117.97 3.66 9.90e-01 1.02e+00 1.37e+01 angle pdb=" C SER B 524 " pdb=" N VAL B 525 " pdb=" CA VAL B 525 " ideal model delta sigma weight residual 122.93 118.36 4.57 1.26e+00 6.30e-01 1.31e+01 angle pdb=" CA ILE B 523 " pdb=" C ILE B 523 " pdb=" O ILE B 523 " ideal model delta sigma weight residual 121.23 117.65 3.58 1.07e+00 8.73e-01 1.12e+01 angle pdb=" C CYS A 591 " pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 122.94 118.00 4.94 1.50e+00 4.44e-01 1.08e+01 angle pdb=" CA SER B 515 " pdb=" C SER B 515 " pdb=" O SER B 515 " ideal model delta sigma weight residual 120.89 117.42 3.47 1.10e+00 8.26e-01 9.92e+00 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 6496 17.02 - 34.04: 621 34.04 - 51.06: 161 51.06 - 68.07: 36 68.07 - 85.09: 12 Dihedral angle restraints: 7326 sinusoidal: 2370 harmonic: 4956 Sorted by residual: dihedral pdb=" CB CYS B 315 " pdb=" SG CYS B 315 " pdb=" SG CYS B 362 " pdb=" CB CYS B 362 " ideal model delta sinusoidal sigma weight residual -86.00 -171.09 85.09 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 362 " pdb=" CB CYS A 362 " ideal model delta sinusoidal sigma weight residual -86.00 -171.09 85.09 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS C 315 " pdb=" SG CYS C 315 " pdb=" SG CYS C 362 " pdb=" CB CYS C 362 " ideal model delta sinusoidal sigma weight residual -86.00 -171.08 85.08 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 7323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1655 0.052 - 0.105: 329 0.105 - 0.157: 66 0.157 - 0.209: 4 0.209 - 0.261: 4 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CA VAL C 519 " pdb=" N VAL C 519 " pdb=" C VAL C 519 " pdb=" CB VAL C 519 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA VAL B 519 " pdb=" N VAL B 519 " pdb=" C VAL B 519 " pdb=" CB VAL B 519 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL B 514 " pdb=" N VAL B 514 " pdb=" C VAL B 514 " pdb=" CB VAL B 514 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2055 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 517 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LYS C 517 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS C 517 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C 518 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 490 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" CG ASP A 490 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP A 490 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 490 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 490 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" CG ASP B 490 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP B 490 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP B 490 " -0.009 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3954 2.82 - 3.34: 11050 3.34 - 3.86: 18171 3.86 - 4.38: 18982 4.38 - 4.90: 34396 Nonbonded interactions: 86553 Sorted by model distance: nonbonded pdb=" OG SER A 263 " pdb=" OE1 GLN A 271 " model vdw 2.298 3.040 nonbonded pdb=" OG SER B 263 " pdb=" OE1 GLN B 271 " model vdw 2.298 3.040 nonbonded pdb=" OG SER C 263 " pdb=" OE1 GLN C 271 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 535 " pdb=" OG SER A 535 " model vdw 2.319 3.040 nonbonded pdb=" O SER C 535 " pdb=" OG SER C 535 " model vdw 2.319 3.040 ... (remaining 86548 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 53 through 492 or (resid 493 and (name N or name CA or nam \ e C or name O or name CB )) or resid 494 through 653)) selection = (chain 'B' and (resid 53 through 492 or (resid 493 and (name N or name CA or nam \ e C or name O or name CB )) or resid 494 through 653)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 29.210 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12300 Z= 0.178 Angle : 0.512 8.417 16893 Z= 0.301 Chirality : 0.045 0.261 2058 Planarity : 0.002 0.035 2202 Dihedral : 15.017 72.945 4065 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 29.66 % Favored : 70.34 % 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: -0.61 (0.21), residues: 1662 helix: 2.98 (0.33), residues: 270 sheet: -0.45 (0.26), residues: 414 loop : -1.44 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 494 HIS 0.002 0.000 HIS B 392 PHE 0.006 0.001 PHE C 518 TYR 0.007 0.001 TYR B 495 ARG 0.002 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.20925 ( 437) hydrogen bonds : angle 7.71440 ( 1332) SS BOND : bond 0.00116 ( 9) SS BOND : angle 1.25127 ( 18) covalent geometry : bond 0.00277 (12291) covalent geometry : angle 0.51027 (16875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 1.456 Fit side-chains REVERT: A 493 MET cc_start: 0.9014 (ttp) cc_final: 0.8770 (ttm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1525 time to fit residues: 8.5285 Evaluate side-chains 18 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN B 583 GLN C 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.070029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.043065 restraints weight = 48567.478| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.17 r_work: 0.2583 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12300 Z= 0.267 Angle : 0.524 4.701 16893 Z= 0.290 Chirality : 0.043 0.151 2058 Planarity : 0.003 0.029 2202 Dihedral : 3.625 20.313 1782 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.10 % Allowed : 28.12 % Favored : 68.79 % 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: -0.83 (0.21), residues: 1662 helix: 2.43 (0.31), residues: 270 sheet: -0.53 (0.25), residues: 444 loop : -1.52 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 305 HIS 0.008 0.001 HIS A 93 PHE 0.010 0.001 PHE C 518 TYR 0.010 0.001 TYR A 390 ARG 0.003 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.05870 ( 437) hydrogen bonds : angle 5.15020 ( 1332) SS BOND : bond 0.00264 ( 9) SS BOND : angle 1.49987 ( 18) covalent geometry : bond 0.00615 (12291) covalent geometry : angle 0.52202 (16875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 21 time to evaluate : 1.394 Fit side-chains REVERT: B 223 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: B 518 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8678 (m-80) outliers start: 36 outliers final: 19 residues processed: 57 average time/residue: 0.1636 time to fit residues: 16.8082 Evaluate side-chains 39 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 18 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 362 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.071832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044622 restraints weight = 48951.404| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 4.31 r_work: 0.2633 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12300 Z= 0.092 Angle : 0.438 5.274 16893 Z= 0.236 Chirality : 0.042 0.143 2058 Planarity : 0.002 0.026 2202 Dihedral : 3.249 14.051 1782 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.92 % Allowed : 28.12 % Favored : 68.96 % 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: -0.63 (0.20), residues: 1662 helix: 2.78 (0.33), residues: 267 sheet: -0.34 (0.26), residues: 417 loop : -1.44 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 401 HIS 0.002 0.000 HIS B 93 PHE 0.008 0.001 PHE C 238 TYR 0.006 0.001 TYR A 101 ARG 0.001 0.000 ARG A 481 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 437) hydrogen bonds : angle 4.49952 ( 1332) SS BOND : bond 0.00126 ( 9) SS BOND : angle 0.91776 ( 18) covalent geometry : bond 0.00192 (12291) covalent geometry : angle 0.43766 (16875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 22 time to evaluate : 1.447 Fit side-chains REVERT: A 490 ASP cc_start: 0.9074 (t0) cc_final: 0.8794 (t0) REVERT: C 490 ASP cc_start: 0.8930 (t0) cc_final: 0.8708 (t0) outliers start: 34 outliers final: 23 residues processed: 56 average time/residue: 0.1564 time to fit residues: 16.0911 Evaluate side-chains 43 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 20 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 621 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 81 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 161 optimal weight: 0.5980 chunk 122 optimal weight: 30.0000 chunk 11 optimal weight: 0.2980 chunk 65 optimal weight: 50.0000 chunk 108 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.070601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.043491 restraints weight = 48405.984| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 4.27 r_work: 0.2598 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12300 Z= 0.175 Angle : 0.460 5.546 16893 Z= 0.248 Chirality : 0.042 0.133 2058 Planarity : 0.003 0.030 2202 Dihedral : 3.439 17.262 1782 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.10 % Allowed : 28.46 % Favored : 68.44 % 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: -0.68 (0.20), residues: 1662 helix: 2.64 (0.32), residues: 267 sheet: -0.47 (0.25), residues: 444 loop : -1.41 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 305 HIS 0.005 0.001 HIS B 93 PHE 0.009 0.001 PHE C 238 TYR 0.007 0.001 TYR C 458 ARG 0.002 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 437) hydrogen bonds : angle 4.49703 ( 1332) SS BOND : bond 0.00177 ( 9) SS BOND : angle 1.27905 ( 18) covalent geometry : bond 0.00401 (12291) covalent geometry : angle 0.45839 (16875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 21 time to evaluate : 1.391 Fit side-chains REVERT: A 490 ASP cc_start: 0.9155 (t0) cc_final: 0.8817 (t0) REVERT: B 163 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7555 (p) REVERT: B 621 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8277 (pt) REVERT: C 163 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7634 (p) REVERT: C 490 ASP cc_start: 0.9024 (t0) cc_final: 0.8744 (t0) outliers start: 36 outliers final: 27 residues processed: 57 average time/residue: 0.1521 time to fit residues: 16.0082 Evaluate side-chains 50 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 20 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 621 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 50.0000 chunk 97 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 110 optimal weight: 40.0000 chunk 138 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.070614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.043553 restraints weight = 48459.570| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 4.26 r_work: 0.2599 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12300 Z= 0.162 Angle : 0.452 6.003 16893 Z= 0.243 Chirality : 0.042 0.131 2058 Planarity : 0.003 0.026 2202 Dihedral : 3.459 16.608 1782 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.78 % Allowed : 27.60 % Favored : 68.62 % 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: -0.68 (0.20), residues: 1662 helix: 2.65 (0.32), residues: 267 sheet: -0.46 (0.25), residues: 444 loop : -1.41 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 305 HIS 0.005 0.001 HIS C 93 PHE 0.009 0.001 PHE C 238 TYR 0.006 0.001 TYR A 390 ARG 0.002 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 437) hydrogen bonds : angle 4.43025 ( 1332) SS BOND : bond 0.00160 ( 9) SS BOND : angle 1.26527 ( 18) covalent geometry : bond 0.00371 (12291) covalent geometry : angle 0.45063 (16875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 21 time to evaluate : 1.355 Fit side-chains REVERT: A 490 ASP cc_start: 0.9173 (t0) cc_final: 0.8810 (t0) REVERT: B 163 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7584 (p) REVERT: B 490 ASP cc_start: 0.9071 (t0) cc_final: 0.8840 (t0) REVERT: C 163 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7613 (p) REVERT: C 220 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8764 (t) REVERT: C 490 ASP cc_start: 0.9066 (t0) cc_final: 0.8767 (t0) outliers start: 44 outliers final: 35 residues processed: 65 average time/residue: 0.1451 time to fit residues: 17.3159 Evaluate side-chains 59 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 21 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 621 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 104 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 131 optimal weight: 0.0070 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.071388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.044258 restraints weight = 48641.568| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.26 r_work: 0.2623 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12300 Z= 0.108 Angle : 0.443 6.672 16893 Z= 0.235 Chirality : 0.042 0.133 2058 Planarity : 0.003 0.027 2202 Dihedral : 3.386 17.432 1782 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.78 % Allowed : 27.60 % Favored : 68.62 % 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: -0.55 (0.20), residues: 1662 helix: 2.72 (0.32), residues: 267 sheet: 0.09 (0.27), residues: 384 loop : -1.51 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 401 HIS 0.003 0.001 HIS B 93 PHE 0.009 0.001 PHE A 238 TYR 0.006 0.001 TYR A 101 ARG 0.001 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 437) hydrogen bonds : angle 4.23883 ( 1332) SS BOND : bond 0.00624 ( 9) SS BOND : angle 1.62617 ( 18) covalent geometry : bond 0.00240 (12291) covalent geometry : angle 0.44029 (16875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 23 time to evaluate : 1.412 Fit side-chains REVERT: A 220 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8921 (t) REVERT: A 490 ASP cc_start: 0.9109 (t0) cc_final: 0.8744 (t0) REVERT: B 163 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7620 (p) REVERT: B 220 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8858 (t) REVERT: B 490 ASP cc_start: 0.9061 (t0) cc_final: 0.8791 (t0) REVERT: C 163 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7638 (p) REVERT: C 220 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8810 (t) REVERT: C 490 ASP cc_start: 0.9018 (t0) cc_final: 0.8721 (t0) outliers start: 44 outliers final: 33 residues processed: 67 average time/residue: 0.1541 time to fit residues: 18.8604 Evaluate side-chains 59 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 21 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 518 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 621 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 0.0770 chunk 44 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 164 optimal weight: 0.0770 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.071343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044414 restraints weight = 48614.165| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 4.25 r_work: 0.2627 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12300 Z= 0.111 Angle : 0.435 7.268 16893 Z= 0.230 Chirality : 0.041 0.131 2058 Planarity : 0.002 0.027 2202 Dihedral : 3.317 18.579 1782 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.70 % Allowed : 27.69 % Favored : 68.62 % 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: -0.53 (0.20), residues: 1662 helix: 2.79 (0.32), residues: 267 sheet: 0.11 (0.26), residues: 384 loop : -1.50 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 401 HIS 0.003 0.001 HIS B 93 PHE 0.009 0.001 PHE A 238 TYR 0.006 0.001 TYR A 101 ARG 0.002 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 437) hydrogen bonds : angle 4.16772 ( 1332) SS BOND : bond 0.00105 ( 9) SS BOND : angle 1.59954 ( 18) covalent geometry : bond 0.00250 (12291) covalent geometry : angle 0.43223 (16875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 21 time to evaluate : 1.429 Fit side-chains REVERT: A 490 ASP cc_start: 0.9120 (t0) cc_final: 0.8755 (t0) REVERT: B 220 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8856 (t) REVERT: B 490 ASP cc_start: 0.9067 (t0) cc_final: 0.8830 (t0) REVERT: C 163 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7643 (p) REVERT: C 220 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8739 (t) REVERT: C 490 ASP cc_start: 0.9028 (t0) cc_final: 0.8736 (t0) outliers start: 43 outliers final: 35 residues processed: 64 average time/residue: 0.1519 time to fit residues: 17.8061 Evaluate side-chains 59 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 21 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 518 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 580 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 6 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.069918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.042727 restraints weight = 48982.967| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.24 r_work: 0.2576 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12300 Z= 0.239 Angle : 0.500 7.840 16893 Z= 0.269 Chirality : 0.042 0.131 2058 Planarity : 0.003 0.033 2202 Dihedral : 3.728 20.618 1782 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.96 % Allowed : 27.34 % Favored : 68.70 % 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: -0.70 (0.20), residues: 1662 helix: 2.47 (0.32), residues: 270 sheet: -0.15 (0.26), residues: 414 loop : -1.54 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 305 HIS 0.007 0.001 HIS B 93 PHE 0.010 0.001 PHE A 238 TYR 0.008 0.001 TYR A 390 ARG 0.003 0.000 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 437) hydrogen bonds : angle 4.43099 ( 1332) SS BOND : bond 0.00198 ( 9) SS BOND : angle 2.32834 ( 18) covalent geometry : bond 0.00549 (12291) covalent geometry : angle 0.49416 (16875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 22 time to evaluate : 1.346 Fit side-chains REVERT: A 490 ASP cc_start: 0.9203 (t0) cc_final: 0.8983 (t0) REVERT: B 220 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8850 (t) REVERT: B 490 ASP cc_start: 0.9150 (t0) cc_final: 0.8853 (t0) REVERT: C 163 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7628 (p) REVERT: C 220 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8681 (t) REVERT: C 490 ASP cc_start: 0.9187 (t0) cc_final: 0.8872 (t0) outliers start: 46 outliers final: 37 residues processed: 68 average time/residue: 0.1337 time to fit residues: 17.2118 Evaluate side-chains 61 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 21 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 518 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 621 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.070143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042927 restraints weight = 48940.594| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 4.25 r_work: 0.2582 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12300 Z= 0.201 Angle : 0.476 8.201 16893 Z= 0.254 Chirality : 0.042 0.130 2058 Planarity : 0.003 0.030 2202 Dihedral : 3.671 17.227 1782 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.78 % Allowed : 27.77 % Favored : 68.44 % 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: -0.69 (0.20), residues: 1662 helix: 2.59 (0.32), residues: 267 sheet: -0.16 (0.25), residues: 414 loop : -1.54 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 305 HIS 0.006 0.001 HIS B 93 PHE 0.010 0.001 PHE A 238 TYR 0.007 0.001 TYR A 390 ARG 0.003 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 437) hydrogen bonds : angle 4.36198 ( 1332) SS BOND : bond 0.00145 ( 9) SS BOND : angle 1.46138 ( 18) covalent geometry : bond 0.00462 (12291) covalent geometry : angle 0.47365 (16875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 22 time to evaluate : 1.560 Fit side-chains REVERT: A 490 ASP cc_start: 0.9192 (t0) cc_final: 0.8842 (t0) REVERT: B 220 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8848 (t) REVERT: B 490 ASP cc_start: 0.9145 (t0) cc_final: 0.8835 (t0) REVERT: C 163 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7619 (p) REVERT: C 220 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8665 (t) REVERT: C 490 ASP cc_start: 0.9147 (t0) cc_final: 0.8851 (t0) outliers start: 44 outliers final: 38 residues processed: 66 average time/residue: 0.1438 time to fit residues: 18.3634 Evaluate side-chains 62 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 21 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 518 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 159 optimal weight: 10.0000 chunk 125 optimal weight: 40.0000 chunk 147 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 136 optimal weight: 0.0870 chunk 132 optimal weight: 0.0050 chunk 145 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN B 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.072167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045401 restraints weight = 48310.750| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.26 r_work: 0.2657 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12300 Z= 0.083 Angle : 0.445 8.731 16893 Z= 0.231 Chirality : 0.042 0.140 2058 Planarity : 0.003 0.029 2202 Dihedral : 3.250 18.250 1782 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.41 % Allowed : 29.15 % Favored : 68.44 % 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: -0.51 (0.20), residues: 1662 helix: 2.87 (0.33), residues: 267 sheet: 0.12 (0.26), residues: 366 loop : -1.49 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 494 HIS 0.003 0.000 HIS C 392 PHE 0.008 0.001 PHE A 238 TYR 0.008 0.001 TYR A 101 ARG 0.004 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 437) hydrogen bonds : angle 3.97024 ( 1332) SS BOND : bond 0.00109 ( 9) SS BOND : angle 1.69085 ( 18) covalent geometry : bond 0.00177 (12291) covalent geometry : angle 0.44175 (16875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 23 time to evaluate : 1.355 Fit side-chains REVERT: A 490 ASP cc_start: 0.9116 (t0) cc_final: 0.8749 (t0) REVERT: B 220 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8763 (t) REVERT: B 490 ASP cc_start: 0.9066 (t0) cc_final: 0.8750 (t0) REVERT: C 163 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7677 (p) REVERT: C 220 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8669 (t) REVERT: C 490 ASP cc_start: 0.8985 (t0) cc_final: 0.8684 (t0) outliers start: 28 outliers final: 25 residues processed: 51 average time/residue: 0.1314 time to fit residues: 13.3327 Evaluate side-chains 49 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 21 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 518 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 580 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 40.0000 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 152 optimal weight: 7.9990 chunk 63 optimal weight: 30.0000 chunk 153 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.068617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.041360 restraints weight = 48925.733| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 4.18 r_work: 0.2534 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 12300 Z= 0.436 Angle : 0.635 8.003 16893 Z= 0.345 Chirality : 0.044 0.136 2058 Planarity : 0.004 0.043 2202 Dihedral : 4.288 22.433 1782 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.70 % Favored : 92.24 % Rotamer: Outliers : 3.27 % Allowed : 28.29 % Favored : 68.44 % 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: -0.94 (0.20), residues: 1662 helix: 2.09 (0.31), residues: 270 sheet: -0.23 (0.25), residues: 441 loop : -1.71 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 305 HIS 0.013 0.002 HIS B 93 PHE 0.012 0.002 PHE B 335 TYR 0.016 0.001 TYR B 360 ARG 0.005 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.06372 ( 437) hydrogen bonds : angle 4.82318 ( 1332) SS BOND : bond 0.00318 ( 9) SS BOND : angle 2.73888 ( 18) covalent geometry : bond 0.01001 (12291) covalent geometry : angle 0.62930 (16875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6295.62 seconds wall clock time: 109 minutes 39.99 seconds (6579.99 seconds total)