Starting phenix.real_space_refine on Wed Sep 17 23:22:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y48_38910/09_2025/8y48_38910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y48_38910/09_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_38910/09_2025/8y48_38910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y48_38910/09_2025/8y48_38910.map" model { file = "/net/cci-nas-00/data/ceres_data/8y48_38910/09_2025/8y48_38910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y48_38910/09_2025/8y48_38910.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 13, 'ASP:plan': 12, 'TYR:plan': 11, 'ARG:plan': 8, 'HIS:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'PHE:plan': 5} 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: {'GLU:plan': 13, 'ASP:plan': 12, 'TYR:plan': 11, 'ARG:plan': 8, 'HIS:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'PHE:plan': 5} 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: {'GLU:plan': 13, 'ASP:plan': 12, 'TYR:plan': 11, 'ARG:plan': 8, 'HIS:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 270 Time building chain proxies: 3.05, per 1000 atoms: 0.25 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: 0.98 Conformation dependent library (CDL) restraints added in 439.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.52 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: 1.92 Time building geometry restraints manager: 1.33 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: 3.770 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.150 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- 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 : 6.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG B 66 TYR 0.007 0.001 TYR B 495 PHE 0.006 0.001 PHE C 518 TRP 0.005 0.001 TRP B 494 HIS 0.002 0.000 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00277 (12291) covalent geometry : angle 0.51027 (16875) SS BOND : bond 0.00116 ( 9) SS BOND : angle 1.25127 ( 18) hydrogen bonds : bond 0.20925 ( 437) hydrogen bonds : angle 7.71440 ( 1332) *********************** 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 : 0.473 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: 0.0665 time to fit residues: 3.6109 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 : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.0390 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.071408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044120 restraints weight = 48785.499| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.28 r_work: 0.2621 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12300 Z= 0.150 Angle : 0.461 4.647 16893 Z= 0.254 Chirality : 0.042 0.158 2058 Planarity : 0.003 0.027 2202 Dihedral : 3.219 15.860 1782 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.15 % Allowed : 28.03 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.21), residues: 1662 helix: 2.73 (0.32), residues: 270 sheet: -0.28 (0.27), residues: 399 loop : -1.44 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 481 TYR 0.007 0.001 TYR B 458 PHE 0.012 0.001 PHE C 518 TRP 0.011 0.001 TRP C 305 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00339 (12291) covalent geometry : angle 0.45993 (16875) SS BOND : bond 0.00156 ( 9) SS BOND : angle 1.08581 ( 18) hydrogen bonds : bond 0.05242 ( 437) hydrogen bonds : angle 5.00158 ( 1332) *********************** 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 46 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 21 time to evaluate : 0.441 Fit side-chains REVERT: B 518 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8562 (m-80) outliers start: 25 outliers final: 12 residues processed: 46 average time/residue: 0.0793 time to fit residues: 6.5559 Evaluate side-chains 33 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL 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 542 LEU Chi-restraints excluded: chain B residue 246 VAL 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 246 VAL 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 80 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 160 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.069884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042576 restraints weight = 49423.239| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 4.26 r_work: 0.2570 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12300 Z= 0.266 Angle : 0.513 4.679 16893 Z= 0.281 Chirality : 0.043 0.140 2058 Planarity : 0.003 0.026 2202 Dihedral : 3.729 19.965 1782 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.21 % Allowed : 26.74 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.20), residues: 1662 helix: 2.35 (0.32), residues: 270 sheet: -0.42 (0.26), residues: 420 loop : -1.57 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 611 TYR 0.009 0.001 TYR A 390 PHE 0.009 0.001 PHE C 335 TRP 0.011 0.002 TRP C 305 HIS 0.008 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00616 (12291) covalent geometry : angle 0.51018 (16875) SS BOND : bond 0.00287 ( 9) SS BOND : angle 1.63556 ( 18) hydrogen bonds : bond 0.05886 ( 437) hydrogen bonds : angle 4.92600 ( 1332) *********************** 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 70 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 21 time to evaluate : 0.394 Fit side-chains REVERT: B 518 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8834 (m-80) outliers start: 49 outliers final: 31 residues processed: 70 average time/residue: 0.0650 time to fit residues: 8.1856 Evaluate side-chains 50 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 18 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL 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 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 B residue 187 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 518 PHE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 187 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 329 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 24 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.071453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.044437 restraints weight = 48545.353| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 4.30 r_work: 0.2628 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1339 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= 0.093 Angle : 0.438 5.823 16893 Z= 0.235 Chirality : 0.042 0.138 2058 Planarity : 0.002 0.026 2202 Dihedral : 3.321 14.364 1782 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.24 % Allowed : 29.49 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.20), residues: 1662 helix: 2.77 (0.33), residues: 267 sheet: -0.42 (0.25), residues: 441 loop : -1.39 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 611 TYR 0.007 0.001 TYR A 101 PHE 0.008 0.001 PHE C 238 TRP 0.008 0.001 TRP C 401 HIS 0.002 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00197 (12291) covalent geometry : angle 0.43733 (16875) SS BOND : bond 0.00118 ( 9) SS BOND : angle 1.03909 ( 18) hydrogen bonds : bond 0.04657 ( 437) hydrogen bonds : angle 4.38717 ( 1332) *********************** 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 47 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 21 time to evaluate : 0.474 Fit side-chains REVERT: B 163 VAL cc_start: 0.7762 (OUTLIER) cc_final: 0.7554 (p) REVERT: B 518 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8811 (m-80) REVERT: C 163 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7638 (p) outliers start: 26 outliers final: 21 residues processed: 47 average time/residue: 0.0693 time to fit residues: 6.0530 Evaluate side-chains 43 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 19 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 VAL 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 B residue 93 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 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 518 PHE 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 218 THR Chi-restraints excluded: chain C residue 239 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 621 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 50.0000 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.069896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.042801 restraints weight = 48803.748| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.25 r_work: 0.2575 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12300 Z= 0.233 Angle : 0.489 6.054 16893 Z= 0.266 Chirality : 0.042 0.133 2058 Planarity : 0.003 0.030 2202 Dihedral : 3.654 18.801 1782 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.21 % Allowed : 27.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1662 helix: 2.44 (0.32), residues: 270 sheet: -0.24 (0.26), residues: 414 loop : -1.53 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 611 TYR 0.008 0.001 TYR A 390 PHE 0.009 0.001 PHE C 238 TRP 0.009 0.002 TRP C 305 HIS 0.007 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00537 (12291) covalent geometry : angle 0.48689 (16875) SS BOND : bond 0.00229 ( 9) SS BOND : angle 1.51355 ( 18) hydrogen bonds : bond 0.05472 ( 437) hydrogen bonds : angle 4.60195 ( 1332) *********************** 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 70 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 21 time to evaluate : 0.416 Fit side-chains REVERT: B 163 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7534 (p) REVERT: B 220 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8819 (t) REVERT: B 490 ASP cc_start: 0.9100 (t0) cc_final: 0.8886 (t0) REVERT: C 163 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7602 (p) outliers start: 49 outliers final: 38 residues processed: 70 average time/residue: 0.0699 time to fit residues: 8.8236 Evaluate side-chains 60 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 19 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 580 THR Chi-restraints excluded: chain B residue 85 CYS 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 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 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 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 329 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 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 70 optimal weight: 0.0060 chunk 76 optimal weight: 0.4980 chunk 41 optimal weight: 0.0050 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 overall best weight: 0.7014 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.071763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044802 restraints weight = 49024.305| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 4.27 r_work: 0.2639 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1490 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= 0.086 Angle : 0.433 6.413 16893 Z= 0.229 Chirality : 0.041 0.134 2058 Planarity : 0.002 0.025 2202 Dihedral : 3.270 12.983 1782 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.35 % Allowed : 28.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.20), residues: 1662 helix: 2.85 (0.33), residues: 267 sheet: -0.12 (0.26), residues: 411 loop : -1.44 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 611 TYR 0.006 0.001 TYR A 101 PHE 0.008 0.001 PHE A 238 TRP 0.008 0.001 TRP C 401 HIS 0.002 0.000 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00181 (12291) covalent geometry : angle 0.43166 (16875) SS BOND : bond 0.00078 ( 9) SS BOND : angle 1.01184 ( 18) hydrogen bonds : bond 0.04322 ( 437) hydrogen bonds : angle 4.19254 ( 1332) *********************** 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 60 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 21 time to evaluate : 0.521 Fit side-chains REVERT: A 220 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8877 (t) REVERT: B 163 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7602 (p) REVERT: B 220 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8873 (t) REVERT: C 163 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7629 (p) REVERT: C 220 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8773 (t) outliers start: 39 outliers final: 28 residues processed: 60 average time/residue: 0.0690 time to fit residues: 7.3244 Evaluate side-chains 52 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 19 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 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 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 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 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 32 optimal weight: 6.9990 chunk 96 optimal weight: 0.0030 chunk 44 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 108 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.070603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.043534 restraints weight = 48541.999| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 4.24 r_work: 0.2600 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1559 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= 0.164 Angle : 0.456 7.256 16893 Z= 0.244 Chirality : 0.041 0.131 2058 Planarity : 0.003 0.031 2202 Dihedral : 3.410 16.308 1782 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1662 helix: 2.73 (0.32), residues: 267 sheet: -0.37 (0.25), residues: 444 loop : -1.39 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 611 TYR 0.007 0.001 TYR B 458 PHE 0.009 0.001 PHE C 238 TRP 0.008 0.001 TRP C 305 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00378 (12291) covalent geometry : angle 0.45419 (16875) SS BOND : bond 0.00149 ( 9) SS BOND : angle 1.28505 ( 18) hydrogen bonds : bond 0.04877 ( 437) hydrogen bonds : angle 4.28262 ( 1332) *********************** 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 65 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 21 time to evaluate : 0.467 Fit side-chains REVERT: B 220 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8841 (t) REVERT: C 163 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7653 (p) REVERT: C 220 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8847 (t) outliers start: 44 outliers final: 37 residues processed: 65 average time/residue: 0.0747 time to fit residues: 8.6883 Evaluate side-chains 59 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 19 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL 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 241 SER Chi-restraints excluded: chain A residue 246 VAL 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 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 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 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 329 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 84 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 148 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 = 0.071403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.044519 restraints weight = 48377.009| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.24 r_work: 0.2630 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1568 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= 0.100 Angle : 0.436 7.829 16893 Z= 0.230 Chirality : 0.041 0.131 2058 Planarity : 0.002 0.025 2202 Dihedral : 3.253 13.529 1782 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.87 % Allowed : 27.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.20), residues: 1662 helix: 2.79 (0.33), residues: 267 sheet: 0.16 (0.26), residues: 381 loop : -1.49 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 611 TYR 0.006 0.001 TYR A 101 PHE 0.009 0.001 PHE C 238 TRP 0.006 0.001 TRP C 401 HIS 0.002 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00222 (12291) covalent geometry : angle 0.43465 (16875) SS BOND : bond 0.00076 ( 9) SS BOND : angle 1.06295 ( 18) hydrogen bonds : bond 0.04367 ( 437) hydrogen bonds : angle 4.05431 ( 1332) *********************** 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 66 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 21 time to evaluate : 0.381 Fit side-chains REVERT: B 220 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8827 (t) REVERT: C 163 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7658 (p) REVERT: C 220 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8788 (t) outliers start: 45 outliers final: 39 residues processed: 66 average time/residue: 0.0735 time to fit residues: 8.6701 Evaluate side-chains 62 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 20 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL 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 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 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 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 C residue 67 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 137 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.070380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.043332 restraints weight = 48475.793| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.24 r_work: 0.2588 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12300 Z= 0.191 Angle : 0.488 8.256 16893 Z= 0.260 Chirality : 0.042 0.136 2058 Planarity : 0.003 0.031 2202 Dihedral : 3.595 20.942 1782 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.20), residues: 1662 helix: 2.64 (0.32), residues: 267 sheet: -0.36 (0.25), residues: 444 loop : -1.42 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 485 TYR 0.007 0.001 TYR C 458 PHE 0.009 0.001 PHE C 238 TRP 0.009 0.001 TRP C 305 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00440 (12291) covalent geometry : angle 0.48089 (16875) SS BOND : bond 0.00207 ( 9) SS BOND : angle 2.56811 ( 18) hydrogen bonds : bond 0.05034 ( 437) hydrogen bonds : angle 4.26680 ( 1332) *********************** 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 72 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 23 time to evaluate : 0.510 Fit side-chains REVERT: B 220 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8813 (t) REVERT: B 647 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: C 163 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7658 (p) REVERT: C 220 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8701 (t) outliers start: 49 outliers final: 41 residues processed: 72 average time/residue: 0.0665 time to fit residues: 9.0575 Evaluate side-chains 63 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 18 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL 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 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 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 647 GLU Chi-restraints excluded: chain C residue 67 VAL 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 329 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 162 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 102 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 67 optimal weight: 0.0170 chunk 46 optimal weight: 20.0000 chunk 130 optimal weight: 0.0970 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.072141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045151 restraints weight = 48625.368| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 4.27 r_work: 0.2655 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12300 Z= 0.084 Angle : 0.443 8.710 16893 Z= 0.232 Chirality : 0.042 0.134 2058 Planarity : 0.002 0.025 2202 Dihedral : 3.185 12.480 1782 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.84 % Allowed : 28.89 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.20), residues: 1662 helix: 2.88 (0.33), residues: 267 sheet: 0.17 (0.26), residues: 381 loop : -1.47 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 485 TYR 0.007 0.001 TYR A 101 PHE 0.009 0.001 PHE A 238 TRP 0.007 0.001 TRP A 494 HIS 0.002 0.000 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00174 (12291) covalent geometry : angle 0.44123 (16875) SS BOND : bond 0.00117 ( 9) SS BOND : angle 1.16105 ( 18) hydrogen bonds : bond 0.04093 ( 437) hydrogen bonds : angle 3.91139 ( 1332) ********************** 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 53 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 20 time to evaluate : 0.546 Fit side-chains REVERT: C 163 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7659 (p) REVERT: C 220 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8692 (t) outliers start: 33 outliers final: 29 residues processed: 53 average time/residue: 0.0659 time to fit residues: 6.6413 Evaluate side-chains 50 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 19 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 93 HIS 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 347 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 218 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 chunk 117 optimal weight: 0.0770 chunk 113 optimal weight: 5.9990 overall best weight: 3.4544 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.069973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042908 restraints weight = 48285.889| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.22 r_work: 0.2579 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12300 Z= 0.228 Angle : 0.491 8.264 16893 Z= 0.266 Chirality : 0.042 0.133 2058 Planarity : 0.003 0.030 2202 Dihedral : 3.602 18.245 1782 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.27 % Allowed : 28.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1662 helix: 2.68 (0.32), residues: 267 sheet: -0.14 (0.25), residues: 414 loop : -1.46 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 611 TYR 0.008 0.001 TYR A 360 PHE 0.010 0.001 PHE C 238 TRP 0.010 0.002 TRP C 305 HIS 0.007 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00523 (12291) covalent geometry : angle 0.48855 (16875) SS BOND : bond 0.00191 ( 9) SS BOND : angle 1.54007 ( 18) hydrogen bonds : bond 0.05329 ( 437) hydrogen bonds : angle 4.28670 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3341.95 seconds wall clock time: 57 minutes 49.95 seconds (3469.95 seconds total)