Starting phenix.real_space_refine on Tue Jun 10 23:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y48_38910/06_2025/8y48_38910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y48_38910/06_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_38910/06_2025/8y48_38910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y48_38910/06_2025/8y48_38910.map" model { file = "/net/cci-nas-00/data/ceres_data/8y48_38910/06_2025/8y48_38910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y48_38910/06_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-5710/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: 8.47, per 1000 atoms: 0.70 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: 2.99 Conformation dependent library (CDL) restraints added in 1.8 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: 1.86 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: 4.26 Time building geometry restraints manager: 3.59 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: 2.180 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.790 Find NCS groups from input model: 0.500 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.340 ------------------------------------------------------------------------------- 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 : 2.033 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: 8.7936 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 : 1.419 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.070037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.043046 restraints weight = 48527.288| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 4.18 r_work: 0.2582 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- 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 : 1.556 Fit side-chains REVERT: B 223 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8030 (tp30) REVERT: B 518 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8677 (m-80) outliers start: 36 outliers final: 19 residues processed: 57 average time/residue: 0.2437 time to fit residues: 26.6756 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 : 1.862 ------------------------------------------------------------------------------- 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: 0.8980 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 30.0000 chunk 74 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.071646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.044408 restraints weight = 49067.141| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 4.31 r_work: 0.2625 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1190 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= 0.101 Angle : 0.441 5.177 16893 Z= 0.238 Chirality : 0.042 0.143 2058 Planarity : 0.002 0.026 2202 Dihedral : 3.282 14.645 1782 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.84 % Allowed : 28.29 % Favored : 68.87 % 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: 2.77 (0.33), residues: 267 sheet: -0.54 (0.25), residues: 447 loop : -1.42 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 401 HIS 0.002 0.000 HIS B 93 PHE 0.007 0.001 PHE C 238 TYR 0.006 0.001 TYR A 101 ARG 0.001 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 437) hydrogen bonds : angle 4.52496 ( 1332) SS BOND : bond 0.00130 ( 9) SS BOND : angle 0.94554 ( 18) covalent geometry : bond 0.00218 (12291) covalent geometry : angle 0.43969 (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 54 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 21 time to evaluate : 1.543 Fit side-chains REVERT: A 490 ASP cc_start: 0.9077 (t0) cc_final: 0.8800 (t0) REVERT: C 490 ASP cc_start: 0.8937 (t0) cc_final: 0.8719 (t0) outliers start: 33 outliers final: 23 residues processed: 54 average time/residue: 0.1650 time to fit residues: 16.5376 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 : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 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 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: 4.9990 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: 7.9990 chunk 122 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 chunk 65 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 ASN C 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.069155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.041851 restraints weight = 48890.677| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.22 r_work: 0.2549 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 12300 Z= 0.356 Angle : 0.567 5.511 16893 Z= 0.311 Chirality : 0.043 0.135 2058 Planarity : 0.004 0.033 2202 Dihedral : 4.004 21.923 1782 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.21 % Allowed : 27.26 % Favored : 68.53 % 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: -0.95 (0.20), residues: 1662 helix: 2.11 (0.31), residues: 270 sheet: -0.33 (0.25), residues: 444 loop : -1.68 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 305 HIS 0.010 0.001 HIS B 93 PHE 0.012 0.001 PHE B 335 TYR 0.013 0.001 TYR A 360 ARG 0.004 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.06142 ( 437) hydrogen bonds : angle 4.93606 ( 1332) SS BOND : bond 0.00336 ( 9) SS BOND : angle 1.90760 ( 18) covalent geometry : bond 0.00822 (12291) covalent geometry : angle 0.56430 (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 70 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 21 time to evaluate : 1.403 Fit side-chains REVERT: C 163 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7558 (p) REVERT: C 499 LYS cc_start: 0.9657 (OUTLIER) cc_final: 0.9349 (tppt) outliers start: 49 outliers final: 38 residues processed: 70 average time/residue: 0.1802 time to fit residues: 21.4017 Evaluate side-chains 58 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 18 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 241 SER 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 499 LYS 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 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 499 LYS 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 85 CYS 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 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 499 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 50.0000 chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 138 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.070867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.043756 restraints weight = 48372.401| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 4.24 r_work: 0.2612 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1501 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= 0.107 Angle : 0.449 6.055 16893 Z= 0.241 Chirality : 0.042 0.135 2058 Planarity : 0.003 0.025 2202 Dihedral : 3.524 15.669 1782 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.70 % Allowed : 27.94 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.75 (0.20), residues: 1662 helix: 2.64 (0.32), residues: 267 sheet: -0.52 (0.25), residues: 444 loop : -1.47 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 401 HIS 0.003 0.001 HIS C 93 PHE 0.007 0.001 PHE B 238 TYR 0.008 0.001 TYR A 101 ARG 0.002 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 437) hydrogen bonds : angle 4.42706 ( 1332) SS BOND : bond 0.00120 ( 9) SS BOND : angle 1.15251 ( 18) covalent geometry : bond 0.00231 (12291) covalent geometry : angle 0.44749 (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 64 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 21 time to evaluate : 1.349 Fit side-chains REVERT: A 220 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8806 (t) REVERT: A 490 ASP cc_start: 0.9089 (t0) cc_final: 0.8837 (t0) REVERT: B 490 ASP cc_start: 0.9057 (t0) cc_final: 0.8821 (t0) REVERT: C 163 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7617 (p) REVERT: C 220 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8749 (t) outliers start: 43 outliers final: 37 residues processed: 64 average time/residue: 0.1473 time to fit residues: 17.3011 Evaluate side-chains 60 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 20 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 220 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 322 THR 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 529 ILE Chi-restraints excluded: chain A residue 597 THR 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 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 621 LEU Chi-restraints excluded: chain C residue 93 HIS 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 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 518 PHE Chi-restraints excluded: chain C residue 529 ILE 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: 8.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 131 optimal weight: 0.0050 chunk 123 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.070806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.043751 restraints weight = 48673.723| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.30 r_work: 0.2608 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12300 Z= 0.126 Angle : 0.444 6.773 16893 Z= 0.237 Chirality : 0.042 0.132 2058 Planarity : 0.003 0.032 2202 Dihedral : 3.416 15.716 1782 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.70 % Allowed : 27.77 % Favored : 68.53 % 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: -0.71 (0.20), residues: 1662 helix: 2.69 (0.32), residues: 267 sheet: -0.47 (0.25), residues: 444 loop : -1.46 (0.19), residues: 951 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 0.008 0.001 PHE B 238 TYR 0.006 0.001 TYR A 101 ARG 0.002 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 437) hydrogen bonds : angle 4.31674 ( 1332) SS BOND : bond 0.00137 ( 9) SS BOND : angle 1.18371 ( 18) covalent geometry : bond 0.00285 (12291) covalent geometry : angle 0.44225 (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 64 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 21 time to evaluate : 1.489 Fit side-chains REVERT: A 220 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8881 (t) REVERT: A 490 ASP cc_start: 0.9113 (t0) cc_final: 0.8812 (t0) REVERT: B 220 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8839 (t) REVERT: B 490 ASP cc_start: 0.9061 (t0) cc_final: 0.8848 (t0) REVERT: C 163 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7641 (p) REVERT: C 220 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8798 (t) outliers start: 43 outliers final: 36 residues processed: 64 average time/residue: 0.1566 time to fit residues: 18.4381 Evaluate side-chains 60 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 20 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 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 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 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 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 239 VAL 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 518 PHE Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 580 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.070130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.042923 restraints weight = 48785.554| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.27 r_work: 0.2586 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1651 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= 0.189 Angle : 0.469 7.415 16893 Z= 0.252 Chirality : 0.042 0.131 2058 Planarity : 0.003 0.028 2202 Dihedral : 3.590 17.309 1782 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.21 % Allowed : 27.69 % Favored : 68.10 % 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: -0.76 (0.20), residues: 1662 helix: 2.58 (0.32), residues: 267 sheet: -0.48 (0.25), residues: 444 loop : -1.50 (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 A 93 PHE 0.009 0.001 PHE B 238 TYR 0.007 0.001 TYR A 390 ARG 0.002 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 437) hydrogen bonds : angle 4.41343 ( 1332) SS BOND : bond 0.00190 ( 9) SS BOND : angle 1.40073 ( 18) covalent geometry : bond 0.00434 (12291) covalent geometry : angle 0.46671 (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 70 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 21 time to evaluate : 1.468 Fit side-chains REVERT: A 220 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8944 (t) REVERT: A 490 ASP cc_start: 0.9155 (t0) cc_final: 0.8855 (t0) REVERT: B 220 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8872 (t) REVERT: B 490 ASP cc_start: 0.9119 (t0) cc_final: 0.8806 (t0) REVERT: B 621 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8215 (pt) REVERT: C 163 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7628 (p) REVERT: C 220 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8720 (t) outliers start: 49 outliers final: 39 residues processed: 70 average time/residue: 0.1549 time to fit residues: 19.9764 Evaluate side-chains 64 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 20 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 329 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 85 CYS 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 241 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 322 THR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 6 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 73 optimal weight: 0.0020 chunk 10 optimal weight: 30.0000 chunk 144 optimal weight: 4.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.070825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.043892 restraints weight = 48564.768| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.23 r_work: 0.2609 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12300 Z= 0.128 Angle : 0.445 7.802 16893 Z= 0.236 Chirality : 0.042 0.131 2058 Planarity : 0.003 0.027 2202 Dihedral : 3.422 15.309 1782 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.04 % Allowed : 28.12 % Favored : 67.84 % 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: -0.67 (0.20), residues: 1662 helix: 2.72 (0.32), residues: 267 sheet: -0.43 (0.24), residues: 444 loop : -1.45 (0.19), residues: 951 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 0.007 0.001 TYR A 101 ARG 0.001 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 437) hydrogen bonds : angle 4.18722 ( 1332) SS BOND : bond 0.00145 ( 9) SS BOND : angle 1.18277 ( 18) covalent geometry : bond 0.00291 (12291) covalent geometry : angle 0.44327 (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: 47 poor density : 21 time to evaluate : 1.425 Fit side-chains REVERT: A 220 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8919 (t) REVERT: A 490 ASP cc_start: 0.9121 (t0) cc_final: 0.8814 (t0) REVERT: B 220 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8849 (t) REVERT: B 490 ASP cc_start: 0.9101 (t0) cc_final: 0.8790 (t0) REVERT: C 163 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7636 (p) REVERT: C 220 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8720 (t) outliers start: 47 outliers final: 39 residues processed: 68 average time/residue: 0.1370 time to fit residues: 17.8338 Evaluate side-chains 63 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 20 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 329 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 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 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 239 VAL 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: 10.0000 chunk 129 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.069580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.042399 restraints weight = 48896.973| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 4.26 r_work: 0.2566 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12300 Z= 0.247 Angle : 0.502 8.130 16893 Z= 0.270 Chirality : 0.042 0.133 2058 Planarity : 0.003 0.034 2202 Dihedral : 3.779 19.087 1782 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.56 % Allowed : 27.52 % Favored : 67.93 % 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: -0.81 (0.20), residues: 1662 helix: 2.36 (0.32), residues: 270 sheet: -0.23 (0.25), residues: 414 loop : -1.60 (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 C 93 PHE 0.010 0.001 PHE A 238 TYR 0.009 0.001 TYR A 360 ARG 0.003 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 437) hydrogen bonds : angle 4.45956 ( 1332) SS BOND : bond 0.00263 ( 9) SS BOND : angle 1.60597 ( 18) covalent geometry : bond 0.00566 (12291) covalent geometry : angle 0.49919 (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 74 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 21 time to evaluate : 1.583 Fit side-chains REVERT: A 220 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8849 (t) REVERT: B 220 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8801 (t) REVERT: B 490 ASP cc_start: 0.9160 (t0) cc_final: 0.8854 (t0) REVERT: C 220 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8669 (t) outliers start: 53 outliers final: 45 residues processed: 74 average time/residue: 0.1882 time to fit residues: 25.7100 Evaluate side-chains 67 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 19 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 241 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 322 THR 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 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 A residue 632 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 85 CYS 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 329 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 620 THR Chi-restraints excluded: chain C residue 85 CYS 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 239 VAL 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=1.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.070808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.043856 restraints weight = 48346.661| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.23 r_work: 0.2609 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12300 Z= 0.109 Angle : 0.450 8.573 16893 Z= 0.238 Chirality : 0.042 0.129 2058 Planarity : 0.003 0.028 2202 Dihedral : 3.453 15.135 1782 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.96 % Allowed : 28.20 % Favored : 67.84 % 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: -0.70 (0.20), residues: 1662 helix: 2.70 (0.32), residues: 267 sheet: -0.45 (0.24), residues: 444 loop : -1.47 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 401 HIS 0.003 0.001 HIS C 392 PHE 0.008 0.001 PHE B 238 TYR 0.008 0.001 TYR A 101 ARG 0.002 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 437) hydrogen bonds : angle 4.15076 ( 1332) SS BOND : bond 0.00118 ( 9) SS BOND : angle 1.18115 ( 18) covalent geometry : bond 0.00242 (12291) covalent geometry : angle 0.44899 (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 67 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 21 time to evaluate : 1.711 Fit side-chains REVERT: A 220 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8824 (t) REVERT: B 220 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8776 (t) REVERT: B 490 ASP cc_start: 0.9099 (t0) cc_final: 0.8790 (t0) REVERT: C 220 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8687 (t) outliers start: 46 outliers final: 39 residues processed: 67 average time/residue: 0.2020 time to fit residues: 26.2007 Evaluate side-chains 61 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 19 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 329 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 B residue 620 THR Chi-restraints excluded: chain C residue 67 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 153 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.069012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.041893 restraints weight = 48711.125| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.20 r_work: 0.2549 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12300 Z= 0.323 Angle : 0.569 8.473 16893 Z= 0.307 Chirality : 0.043 0.139 2058 Planarity : 0.004 0.039 2202 Dihedral : 4.115 21.182 1782 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.46 % Favored : 92.36 % Rotamer: Outliers : 4.30 % Allowed : 27.77 % Favored : 67.93 % 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: -0.93 (0.20), residues: 1662 helix: 2.19 (0.31), residues: 270 sheet: -0.28 (0.25), residues: 444 loop : -1.71 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 305 HIS 0.009 0.001 HIS B 93 PHE 0.010 0.001 PHE C 238 TYR 0.012 0.001 TYR A 360 ARG 0.003 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.05885 ( 437) hydrogen bonds : angle 4.64063 ( 1332) SS BOND : bond 0.00230 ( 9) SS BOND : angle 3.07820 ( 18) covalent geometry : bond 0.00744 (12291) covalent geometry : angle 0.56059 (16875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6754.33 seconds wall clock time: 120 minutes 28.49 seconds (7228.49 seconds total)