Starting phenix.real_space_refine on Thu Jul 2 06:49:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qcu_13899/07_2026/7qcu_13899.cif" } resolution = 3.25 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= 0.007 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 106 5.16 5 C 4393 2.51 5 N 1142 2.21 5 O 1426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7069 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3410 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 34, 'TRANS': 408} Chain breaks: 3 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3423 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 34, 'TRANS': 410} Chain breaks: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.22, per 1000 atoms: 0.17 Number of scatterers: 7069 At special positions: 0 Unit cell: (64.78, 132.02, 121.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 106 16.00 O 1426 8.00 N 1142 7.00 C 4393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A4352 " - pdb=" SG CYS A4386 " distance=2.04 Simple disulfide: pdb=" SG CYS A4379 " - pdb=" SG CYS B4379 " distance=2.29 Simple disulfide: pdb=" SG CYS A4381 " - pdb=" SG CYS A4422 " distance=2.04 Simple disulfide: pdb=" SG CYS A4399 " - pdb=" SG CYS A4423 " distance=2.03 Simple disulfide: pdb=" SG CYS A4407 " - pdb=" SG CYS A4428 " distance=2.02 Simple disulfide: pdb=" SG CYS A4430 " - pdb=" SG CYS A4576 " distance=2.02 Simple disulfide: pdb=" SG CYS A4432 " - pdb=" SG CYS A4573 " distance=2.03 Simple disulfide: pdb=" SG CYS A4454 " - pdb=" SG CYS A4612 " distance=2.00 Simple disulfide: pdb=" SG CYS A4478 " - pdb=" SG CYS A4486 " distance=2.03 Simple disulfide: pdb=" SG CYS A4584 " - pdb=" SG CYS A4595 " distance=2.01 Simple disulfide: pdb=" SG CYS A4638 " - pdb=" SG CYS A4673 " distance=2.03 Simple disulfide: pdb=" SG CYS A4644 " - pdb=" SG CYS A4668 " distance=2.03 Simple disulfide: pdb=" SG CYS A4655 " - pdb=" SG CYS A4692 " distance=2.03 Simple disulfide: pdb=" SG CYS A4682 " - pdb=" SG CYS A4709 " distance=2.04 Simple disulfide: pdb=" SG CYS A4698 " - pdb=" SG CYS A4722 " distance=2.03 Simple disulfide: pdb=" SG CYS A4713 " - pdb=" SG CYS A4746 " distance=2.03 Simple disulfide: pdb=" SG CYS A4730 " - pdb=" SG CYS A4766 " distance=2.06 Simple disulfide: pdb=" SG CYS A4748 " - pdb=" SG CYS A4762 " distance=2.04 Simple disulfide: pdb=" SG CYS A4768 " - pdb=" SG CYS A4791 " distance=2.05 Simple disulfide: pdb=" SG CYS A4786 " - pdb=" SG CYS A4830 " distance=2.03 Simple disulfide: pdb=" SG CYS A4789 " - pdb=" SG CYS A4800 " distance=2.02 Simple disulfide: pdb=" SG CYS A4805 " - pdb=" SG CYS A4831 " distance=2.04 Simple disulfide: pdb=" SG CYS A4813 " - pdb=" SG CYS A4836 " distance=1.92 Simple disulfide: pdb=" SG CYS B4352 " - pdb=" SG CYS B4386 " distance=2.02 Simple disulfide: pdb=" SG CYS B4381 " - pdb=" SG CYS B4422 " distance=2.00 Simple disulfide: pdb=" SG CYS B4399 " - pdb=" SG CYS B4423 " distance=2.03 Simple disulfide: pdb=" SG CYS B4407 " - pdb=" SG CYS B4428 " distance=2.02 Simple disulfide: pdb=" SG CYS B4430 " - pdb=" SG CYS B4576 " distance=2.01 Simple disulfide: pdb=" SG CYS B4432 " - pdb=" SG CYS B4573 " distance=2.03 Simple disulfide: pdb=" SG CYS B4454 " - pdb=" SG CYS B4612 " distance=2.03 Simple disulfide: pdb=" SG CYS B4478 " - pdb=" SG CYS B4486 " distance=2.02 Simple disulfide: pdb=" SG CYS B4584 " - pdb=" SG CYS B4595 " distance=2.03 Simple disulfide: pdb=" SG CYS B4638 " - pdb=" SG CYS B4673 " distance=2.05 Simple disulfide: pdb=" SG CYS B4644 " - pdb=" SG CYS B4668 " distance=2.03 Simple disulfide: pdb=" SG CYS B4655 " - pdb=" SG CYS B4692 " distance=2.03 Simple disulfide: pdb=" SG CYS B4682 " - pdb=" SG CYS B4709 " distance=2.03 Simple disulfide: pdb=" SG CYS B4698 " - pdb=" SG CYS B4722 " distance=2.03 Simple disulfide: pdb=" SG CYS B4713 " - pdb=" SG CYS B4746 " distance=2.03 Simple disulfide: pdb=" SG CYS B4730 " - pdb=" SG CYS B4766 " distance=1.99 Simple disulfide: pdb=" SG CYS B4748 " - pdb=" SG CYS B4762 " distance=2.03 Simple disulfide: pdb=" SG CYS B4768 " - pdb=" SG CYS B4791 " distance=2.03 Simple disulfide: pdb=" SG CYS B4786 " - pdb=" SG CYS B4830 " distance=2.02 Simple disulfide: pdb=" SG CYS B4789 " - pdb=" SG CYS B4800 " distance=2.03 Simple disulfide: pdb=" SG CYS B4805 " - pdb=" SG CYS B4831 " distance=2.03 Simple disulfide: pdb=" SG CYS B4813 " - pdb=" SG CYS B4836 " 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A5202 " - " ASN A4703 " " NAG A5203 " - " ASN A4738 " " NAG A5204 " - " ASN A4567 " " NAG A5205 " - " ASN A4832 " " NAG B5202 " - " ASN B4703 " " NAG B5203 " - " ASN B4738 " " NAG B5204 " - " ASN B4832 " " NAG B5205 " - " ASN B4567 " " NAG C 1 " - " ASN A4578 " " NAG D 1 " - " ASN B4578 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 258.9 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 18 sheets defined 15.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 4580 through 4584 removed outlier: 4.247A pdb=" N CYS A4584 " --> pdb=" O SER A4581 " (cutoff:3.500A) Processing helix chain 'A' and resid 4594 through 4602 removed outlier: 4.254A pdb=" N ASP A4600 " --> pdb=" O GLU A4596 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A4601 " --> pdb=" O ALA A4597 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A4602 " --> pdb=" O ALA A4598 " (cutoff:3.500A) Processing helix chain 'A' and resid 4641 through 4646 Processing helix chain 'A' and resid 4649 through 4651 No H-bonds generated for 'chain 'A' and resid 4649 through 4651' Processing helix chain 'A' and resid 4652 through 4657 removed outlier: 3.954A pdb=" N ALA A4657 " --> pdb=" O ALA A4653 " (cutoff:3.500A) Processing helix chain 'A' and resid 4661 through 4675 removed outlier: 3.638A pdb=" N MET A4675 " --> pdb=" O ASP A4671 " (cutoff:3.500A) Processing helix chain 'A' and resid 4681 through 4695 removed outlier: 3.971A pdb=" N LEU A4685 " --> pdb=" O GLU A4681 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4706 Processing helix chain 'B' and resid 4561 through 4566 Processing helix chain 'B' and resid 4579 through 4583 removed outlier: 3.943A pdb=" N ASP B4582 " --> pdb=" O THR B4579 " (cutoff:3.500A) Processing helix chain 'B' and resid 4594 through 4602 removed outlier: 3.531A pdb=" N ALA B4598 " --> pdb=" O ASN B4594 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B4599 " --> pdb=" O CYS B4595 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B4600 " --> pdb=" O GLU B4596 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B4601 " --> pdb=" O ALA B4597 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B4602 " --> pdb=" O ALA B4598 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4594 through 4602' Processing helix chain 'B' and resid 4642 through 4647 removed outlier: 3.539A pdb=" N ILE B4647 " --> pdb=" O CYS B4644 " (cutoff:3.500A) Processing helix chain 'B' and resid 4649 through 4651 No H-bonds generated for 'chain 'B' and resid 4649 through 4651' Processing helix chain 'B' and resid 4652 through 4657 removed outlier: 4.176A pdb=" N ALA B4657 " --> pdb=" O ALA B4653 " (cutoff:3.500A) Processing helix chain 'B' and resid 4661 through 4675 removed outlier: 3.625A pdb=" N MET B4675 " --> pdb=" O ASP B4671 " (cutoff:3.500A) Processing helix chain 'B' and resid 4682 through 4695 removed outlier: 3.557A pdb=" N GLN B4686 " --> pdb=" O CYS B4682 " (cutoff:3.500A) Processing helix chain 'B' and resid 4702 through 4706 removed outlier: 3.771A pdb=" N HIS B4706 " --> pdb=" O ASN B4703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4382 through 4383 Processing sheet with id=AA2, first strand: chain 'A' and resid 4391 through 4392 removed outlier: 3.641A pdb=" N PHE B4382 " --> pdb=" O LEU B4378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4414 through 4417 Processing sheet with id=AA4, first strand: chain 'A' and resid 4430 through 4435 Processing sheet with id=AA5, first strand: chain 'A' and resid 4439 through 4441 Processing sheet with id=AA6, first strand: chain 'A' and resid 4507 through 4512 removed outlier: 4.539A pdb=" N THR A4503 " --> pdb=" O ARG A4488 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG A4488 " --> pdb=" O THR A4503 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A4473 " --> pdb=" O VAL A4457 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL A4457 " --> pdb=" O ILE A4473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4718 through 4719 Processing sheet with id=AA8, first strand: chain 'A' and resid 4753 through 4754 Processing sheet with id=AA9, first strand: chain 'A' and resid 4780 through 4784 Processing sheet with id=AB1, first strand: chain 'B' and resid 4414 through 4417 Processing sheet with id=AB2, first strand: chain 'B' and resid 4430 through 4435 Processing sheet with id=AB3, first strand: chain 'B' and resid 4439 through 4441 Processing sheet with id=AB4, first strand: chain 'B' and resid 4519 through 4520 removed outlier: 4.639A pdb=" N GLN B4510 " --> pdb=" O VAL B4520 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B4504 " --> pdb=" O MET B4507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR B4503 " --> pdb=" O ARG B4488 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG B4488 " --> pdb=" O THR B4503 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE B4469 " --> pdb=" O GLU B4460 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU B4460 " --> pdb=" O PHE B4469 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B4471 " --> pdb=" O LEU B4458 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 4718 through 4723 removed outlier: 4.166A pdb=" N CYS B4722 " --> pdb=" O VAL B4743 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL B4743 " --> pdb=" O CYS B4722 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 4753 through 4754 Processing sheet with id=AB7, first strand: chain 'B' and resid 4768 through 4769 Processing sheet with id=AB8, first strand: chain 'B' and resid 4781 through 4782 Processing sheet with id=AB9, first strand: chain 'B' and resid 4818 through 4823 204 hydrogen bonds defined for protein. 501 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: 0.80 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1200 1.28 - 1.42: 1787 1.42 - 1.55: 4142 1.55 - 1.69: 4 1.69 - 1.82: 120 Bond restraints: 7253 Sorted by residual: bond pdb=" C GLU A4398 " pdb=" N CYS A4399 " ideal model delta sigma weight residual 1.330 1.525 -0.195 1.22e-02 6.72e+03 2.55e+02 bond pdb=" N PRO A4809 " pdb=" CD PRO A4809 " ideal model delta sigma weight residual 1.473 1.314 0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" C ILE A4491 " pdb=" O ILE A4491 " ideal model delta sigma weight residual 1.238 1.150 0.088 1.10e-02 8.26e+03 6.38e+01 bond pdb=" N PRO A4610 " pdb=" CD PRO A4610 " ideal model delta sigma weight residual 1.473 1.557 -0.084 1.40e-02 5.10e+03 3.61e+01 bond pdb=" C TYR A4562 " pdb=" O TYR A4562 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.16e-02 7.43e+03 3.26e+01 ... (remaining 7248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.08: 9508 5.08 - 10.15: 358 10.15 - 15.23: 34 15.23 - 20.31: 2 20.31 - 25.39: 4 Bond angle restraints: 9906 Sorted by residual: angle pdb=" C ASN A4552 " pdb=" CA ASN A4552 " pdb=" CB ASN A4552 " ideal model delta sigma weight residual 110.24 84.85 25.39 1.88e+00 2.83e-01 1.82e+02 angle pdb=" C THR A4705 " pdb=" CA THR A4705 " pdb=" CB THR A4705 " ideal model delta sigma weight residual 110.01 87.14 22.87 1.80e+00 3.09e-01 1.61e+02 angle pdb=" C GLU A4744 " pdb=" CA GLU A4744 " pdb=" CB GLU A4744 " ideal model delta sigma weight residual 110.51 88.15 22.36 1.89e+00 2.80e-01 1.40e+02 angle pdb=" C THR A4503 " pdb=" CA THR A4503 " pdb=" CB THR A4503 " ideal model delta sigma weight residual 110.14 93.16 16.98 1.60e+00 3.91e-01 1.13e+02 angle pdb=" CA THR B4375 " pdb=" CB THR B4375 " pdb=" OG1 THR B4375 " ideal model delta sigma weight residual 109.60 94.84 14.76 1.50e+00 4.44e-01 9.69e+01 ... (remaining 9901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3795 17.52 - 35.05: 374 35.05 - 52.57: 105 52.57 - 70.10: 26 70.10 - 87.62: 21 Dihedral angle restraints: 4321 sinusoidal: 1735 harmonic: 2586 Sorted by residual: dihedral pdb=" C ASN A4552 " pdb=" N ASN A4552 " pdb=" CA ASN A4552 " pdb=" CB ASN A4552 " ideal model delta harmonic sigma weight residual -122.60 -86.34 -36.26 0 2.50e+00 1.60e-01 2.10e+02 dihedral pdb=" C GLU A4744 " pdb=" N GLU A4744 " pdb=" CA GLU A4744 " pdb=" CB GLU A4744 " ideal model delta harmonic sigma weight residual -122.60 -93.26 -29.34 0 2.50e+00 1.60e-01 1.38e+02 dihedral pdb=" C THR A4705 " pdb=" N THR A4705 " pdb=" CA THR A4705 " pdb=" CB THR A4705 " ideal model delta harmonic sigma weight residual -122.00 -96.66 -25.34 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 4318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.262: 1015 0.262 - 0.524: 106 0.524 - 0.786: 9 0.786 - 1.047: 2 1.047 - 1.309: 1 Chirality restraints: 1133 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 9.57e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.42e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B4578 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.29e+01 ... (remaining 1130 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A5203 " -0.349 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A5203 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A5203 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG A5203 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG A5203 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A5202 " -0.337 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG A5202 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A5202 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG A5202 " 0.515 2.00e-02 2.50e+03 pdb=" O7 NAG A5202 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B5204 " -0.337 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG B5204 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B5204 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG B5204 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG B5204 " -0.158 2.00e-02 2.50e+03 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 67 2.47 - 3.08: 5192 3.08 - 3.69: 11323 3.69 - 4.29: 16214 4.29 - 4.90: 25780 Nonbonded interactions: 58576 Sorted by model distance: nonbonded pdb=" O THR B4503 " pdb=" OG1 THR B4503 " model vdw 1.868 3.040 nonbonded pdb=" OD1 ASP B4583 " pdb="CA CA B5201 " model vdw 1.947 2.510 nonbonded pdb=" O THR A4503 " pdb=" CG2 THR A4503 " model vdw 2.004 3.460 nonbonded pdb=" OG1 THR B4577 " pdb="CA CA B5201 " model vdw 2.041 2.510 nonbonded pdb=" O ASN B4475 " pdb=" OD1 ASN B4475 " model vdw 2.114 3.040 ... (remaining 58571 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' selection = (chain 'B' and (resid 4350 through 4839 or resid 5201 through 5205)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.000 Find NCS groups from input model: 0.070 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 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 : 0.013 0.256 7316 Z= 0.931 Angle : 2.278 26.635 10050 Z= 1.469 Chirality : 0.163 1.309 1133 Planarity : 0.025 0.296 1282 Dihedral : 15.609 85.024 2522 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 6.94 % Allowed : 9.47 % Favored : 83.59 % Cbeta Deviations : 7.81 % 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 are not related in a simple way. whole: -1.89 (0.27), residues: 872 helix: 0.93 (0.67), residues: 66 sheet: -0.74 (0.37), residues: 187 loop : -1.78 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG B4488 TYR 0.065 0.004 TYR A4532 PHE 0.040 0.003 PHE B4782 TRP 0.034 0.005 TRP B4602 HIS 0.012 0.002 HIS B4505 Details of bonding type rmsd/Z covalent geometry : bond 0.01267 / 0.92 ( 7253) covalent geometry : angle 2.17907 / 1.45 ( 9906) SS BOND : bond 0.04390 / 2.88 ( 45) SS BOND : angle 5.17592 / 3.84 ( 90) hydrogen bonds : bond 0.18183 / 10.54 ( 204) hydrogen bonds : angle 9.86054 / 6.65 ( 501) link_ALPHA1-3 : bond 0.00085 / 0.06 ( 2) link_ALPHA1-3 : angle 0.53672 / 0.39 ( 6) link_ALPHA1-6 : bond 0.00241 / 0.17 ( 2) link_ALPHA1-6 : angle 0.75745 / 0.53 ( 6) link_BETA1-4 : bond 0.02405 / 1.38 ( 4) link_BETA1-4 : angle 7.43137 / 3.67 ( 12) link_NAG-ASN : bond 0.01484 / 0.72 ( 10) link_NAG-ASN : angle 8.22724 / 7.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 66 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 13 residues processed: 116 average time/residue: 0.0628 time to fit residues: 10.1263 Evaluate side-chains 41 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4383 MET Chi-restraints excluded: chain A residue 4397 VAL Chi-restraints excluded: chain A residue 4406 THR Chi-restraints excluded: chain A residue 4550 SER Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain A residue 4833 ILE Chi-restraints excluded: chain B residue 4407 CYS Chi-restraints excluded: chain B residue 4768 CYS Chi-restraints excluded: chain B residue 4791 CYS Chi-restraints excluded: chain B residue 4831 CYS Chi-restraints excluded: chain B residue 4832 ASN Chi-restraints excluded: chain B residue 4836 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4686 GLN A4839 ASN B4425 HIS B4439 HIS ** B4505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4801 GLN ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.104252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072616 restraints weight = 20863.324| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 4.94 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 7316 Z= 0.183 Angle : 0.958 14.982 10050 Z= 0.455 Chirality : 0.059 0.629 1133 Planarity : 0.006 0.055 1282 Dihedral : 7.720 59.580 957 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 3.79 % Allowed : 12.25 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -1.57 (0.28), residues: 872 helix: 1.90 (0.65), residues: 66 sheet: -0.55 (0.39), residues: 171 loop : -1.63 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A4564 TYR 0.023 0.001 TYR B4527 PHE 0.023 0.002 PHE B4674 TRP 0.028 0.002 TRP A4376 HIS 0.007 0.001 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 7253) covalent geometry : angle 0.88040 / 0.43 ( 9906) SS BOND : bond 0.00500 / 0.24 ( 45) SS BOND : angle 2.06231 / 1.62 ( 90) hydrogen bonds : bond 0.03965 / 2.43 ( 204) hydrogen bonds : angle 7.54307 / 5.23 ( 501) link_ALPHA1-3 : bond 0.00537 / 0.38 ( 2) link_ALPHA1-3 : angle 1.35306 / 0.98 ( 6) link_ALPHA1-6 : bond 0.00889 / 0.60 ( 2) link_ALPHA1-6 : angle 1.40489 / 0.94 ( 6) link_BETA1-4 : bond 0.00814 / 0.55 ( 4) link_BETA1-4 : angle 4.81688 / 2.41 ( 12) link_NAG-ASN : bond 0.00824 / 0.42 ( 10) link_NAG-ASN : angle 5.38537 / 4.10 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 34 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4428 CYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7139 (p) REVERT: A 4478 CYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6648 (p) REVERT: A 4509 MET cc_start: 0.8770 (ptm) cc_final: 0.8489 (ptp) REVERT: A 4578 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8102 (t0) REVERT: B 4376 TRP cc_start: 0.8597 (m100) cc_final: 0.8219 (m100) REVERT: B 4675 MET cc_start: 0.8366 (pmm) cc_final: 0.8064 (pmm) outliers start: 30 outliers final: 11 residues processed: 63 average time/residue: 0.0525 time to fit residues: 5.0323 Evaluate side-chains 37 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4383 MET Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4478 CYS Chi-restraints excluded: chain A residue 4578 ASN Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4734 SER Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain A residue 4833 ILE Chi-restraints excluded: chain B residue 4395 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4729 THR Chi-restraints excluded: chain B residue 4791 CYS Chi-restraints excluded: chain B residue 4831 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4505 HIS A4739 ASN ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.097194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064923 restraints weight = 20667.856| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 5.01 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7316 Z= 0.183 Angle : 0.908 18.281 10050 Z= 0.415 Chirality : 0.060 0.717 1133 Planarity : 0.006 0.057 1282 Dihedral : 6.530 56.603 949 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.78 % Allowed : 14.90 % Favored : 82.32 % 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 are not related in a simple way. whole: -1.47 (0.28), residues: 872 helix: 2.57 (0.65), residues: 66 sheet: -0.53 (0.39), residues: 175 loop : -1.62 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4564 TYR 0.015 0.001 TYR B4440 PHE 0.015 0.001 PHE B4674 TRP 0.041 0.002 TRP A4376 HIS 0.006 0.001 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 7253) covalent geometry : angle 0.81146 / 0.39 ( 9906) SS BOND : bond 0.00385 / 0.19 ( 45) SS BOND : angle 1.44514 / 1.04 ( 90) hydrogen bonds : bond 0.03455 / 2.12 ( 204) hydrogen bonds : angle 6.96882 / 4.92 ( 501) link_ALPHA1-3 : bond 0.00705 / 0.49 ( 2) link_ALPHA1-3 : angle 1.30202 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00679 / 0.46 ( 2) link_ALPHA1-6 : angle 1.57364 / 0.97 ( 6) link_BETA1-4 : bond 0.00900 / 0.61 ( 4) link_BETA1-4 : angle 3.89133 / 1.84 ( 12) link_NAG-ASN : bond 0.01449 / 0.91 ( 10) link_NAG-ASN : angle 6.76688 / 4.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8961 (mmm) REVERT: A 4478 CYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6703 (p) REVERT: A 4509 MET cc_start: 0.8762 (ptm) cc_final: 0.8517 (ptp) REVERT: B 4376 TRP cc_start: 0.8497 (m100) cc_final: 0.8086 (m100) outliers start: 22 outliers final: 14 residues processed: 49 average time/residue: 0.0510 time to fit residues: 3.9962 Evaluate side-chains 40 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4383 MET Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4478 CYS Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4738 ASN Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4395 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4765 THR Chi-restraints excluded: chain B residue 4768 CYS Chi-restraints excluded: chain B residue 4786 CYS Chi-restraints excluded: chain B residue 4791 CYS Chi-restraints excluded: chain B residue 4831 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 53 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064739 restraints weight = 20802.067| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 5.04 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7316 Z= 0.151 Angle : 0.821 18.313 10050 Z= 0.377 Chirality : 0.055 0.592 1133 Planarity : 0.005 0.060 1282 Dihedral : 6.252 57.326 947 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.89 % Rotamer: Outliers : 3.03 % Allowed : 14.90 % Favored : 82.07 % 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 are not related in a simple way. whole: -1.47 (0.29), residues: 872 helix: 2.82 (0.66), residues: 66 sheet: -0.51 (0.40), residues: 175 loop : -1.67 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4564 TYR 0.013 0.001 TYR B4440 PHE 0.012 0.001 PHE B4674 TRP 0.042 0.002 TRP A4376 HIS 0.006 0.001 HIS B4505 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7253) covalent geometry : angle 0.73518 / 0.36 ( 9906) SS BOND : bond 0.00268 / 0.15 ( 45) SS BOND : angle 1.05866 / 0.69 ( 90) hydrogen bonds : bond 0.03085 / 1.89 ( 204) hydrogen bonds : angle 6.57126 / 4.70 ( 501) link_ALPHA1-3 : bond 0.00571 / 0.40 ( 2) link_ALPHA1-3 : angle 1.42116 / 0.95 ( 6) link_ALPHA1-6 : bond 0.00681 / 0.47 ( 2) link_ALPHA1-6 : angle 1.45270 / 0.92 ( 6) link_BETA1-4 : bond 0.00888 / 0.55 ( 4) link_BETA1-4 : angle 3.88314 / 1.89 ( 12) link_NAG-ASN : bond 0.01432 / 0.82 ( 10) link_NAG-ASN : angle 6.09095 / 4.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4509 MET cc_start: 0.8716 (ptm) cc_final: 0.8487 (ptp) REVERT: B 4376 TRP cc_start: 0.8435 (m100) cc_final: 0.8089 (m100) REVERT: B 4729 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8382 (t) outliers start: 24 outliers final: 13 residues processed: 51 average time/residue: 0.0495 time to fit residues: 3.7875 Evaluate side-chains 38 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4698 CYS Chi-restraints excluded: chain A residue 4738 ASN Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4729 THR Chi-restraints excluded: chain B residue 4765 THR Chi-restraints excluded: chain B residue 4786 CYS Chi-restraints excluded: chain B residue 4791 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.096370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064045 restraints weight = 20911.628| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 5.03 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7316 Z= 0.171 Angle : 0.809 18.576 10050 Z= 0.375 Chirality : 0.054 0.589 1133 Planarity : 0.005 0.063 1282 Dihedral : 5.858 51.324 943 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.90 % Allowed : 16.04 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.28), residues: 872 helix: 3.01 (0.67), residues: 66 sheet: -0.57 (0.40), residues: 175 loop : -1.67 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4564 TYR 0.012 0.001 TYR B4440 PHE 0.011 0.001 PHE B4674 TRP 0.025 0.002 TRP A4377 HIS 0.004 0.001 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 7253) covalent geometry : angle 0.72105 / 0.35 ( 9906) SS BOND : bond 0.00298 / 0.16 ( 45) SS BOND : angle 1.41827 / 0.83 ( 90) hydrogen bonds : bond 0.03119 / 1.91 ( 204) hydrogen bonds : angle 6.37200 / 4.56 ( 501) link_ALPHA1-3 : bond 0.00557 / 0.38 ( 2) link_ALPHA1-3 : angle 1.42310 / 0.98 ( 6) link_ALPHA1-6 : bond 0.00637 / 0.43 ( 2) link_ALPHA1-6 : angle 1.34215 / 0.90 ( 6) link_BETA1-4 : bond 0.00792 / 0.53 ( 4) link_BETA1-4 : angle 3.60959 / 1.77 ( 12) link_NAG-ASN : bond 0.01382 / 0.77 ( 10) link_NAG-ASN : angle 5.95050 / 3.97 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 28 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9255 (tpt) cc_final: 0.8905 (mmt) REVERT: A 4509 MET cc_start: 0.8734 (ptm) cc_final: 0.8526 (ptp) outliers start: 23 outliers final: 18 residues processed: 48 average time/residue: 0.0445 time to fit residues: 3.4126 Evaluate side-chains 39 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 21 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4378 LEU Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4698 CYS Chi-restraints excluded: chain A residue 4738 ASN Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4729 THR Chi-restraints excluded: chain B residue 4765 THR Chi-restraints excluded: chain B residue 4786 CYS Chi-restraints excluded: chain B residue 4791 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 22 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4512 GLN ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.097120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064825 restraints weight = 21011.751| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 5.04 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7316 Z= 0.156 Angle : 0.802 18.415 10050 Z= 0.371 Chirality : 0.054 0.582 1133 Planarity : 0.005 0.063 1282 Dihedral : 5.764 55.796 943 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.65 % Allowed : 17.68 % Favored : 79.67 % 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 are not related in a simple way. whole: -1.47 (0.29), residues: 872 helix: 2.99 (0.66), residues: 66 sheet: -0.65 (0.39), residues: 175 loop : -1.63 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4564 TYR 0.011 0.001 TYR B4440 PHE 0.020 0.001 PHE B4674 TRP 0.023 0.001 TRP A4376 HIS 0.004 0.001 HIS B4505 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7253) covalent geometry : angle 0.71956 / 0.35 ( 9906) SS BOND : bond 0.00264 / 0.14 ( 45) SS BOND : angle 1.26250 / 0.72 ( 90) hydrogen bonds : bond 0.03012 / 1.86 ( 204) hydrogen bonds : angle 6.22228 / 4.48 ( 501) link_ALPHA1-3 : bond 0.00549 / 0.38 ( 2) link_ALPHA1-3 : angle 1.43707 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00682 / 0.46 ( 2) link_ALPHA1-6 : angle 1.33549 / 0.89 ( 6) link_BETA1-4 : bond 0.00810 / 0.54 ( 4) link_BETA1-4 : angle 3.54632 / 1.73 ( 12) link_NAG-ASN : bond 0.01380 / 0.76 ( 10) link_NAG-ASN : angle 5.83954 / 3.86 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9241 (tpt) cc_final: 0.8891 (mmt) REVERT: A 4804 ARG cc_start: 0.8578 (tpm170) cc_final: 0.8361 (tpm170) REVERT: B 4512 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: B 4594 ASN cc_start: 0.8767 (t0) cc_final: 0.8457 (t0) outliers start: 21 outliers final: 16 residues processed: 47 average time/residue: 0.0428 time to fit residues: 3.1810 Evaluate side-chains 42 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4698 CYS Chi-restraints excluded: chain A residue 4738 ASN Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4512 GLN Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4729 THR Chi-restraints excluded: chain B residue 4765 THR Chi-restraints excluded: chain B residue 4786 CYS Chi-restraints excluded: chain B residue 4791 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 0.0370 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.096710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064072 restraints weight = 20705.131| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 5.03 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7316 Z= 0.149 Angle : 0.799 18.412 10050 Z= 0.368 Chirality : 0.054 0.575 1133 Planarity : 0.005 0.066 1282 Dihedral : 5.742 58.722 942 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.40 % Allowed : 17.93 % Favored : 79.67 % 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 are not related in a simple way. whole: -1.47 (0.29), residues: 872 helix: 2.99 (0.66), residues: 66 sheet: -0.64 (0.39), residues: 170 loop : -1.63 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4564 TYR 0.011 0.001 TYR B4440 PHE 0.017 0.001 PHE B4674 TRP 0.022 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 7253) covalent geometry : angle 0.71502 / 0.35 ( 9906) SS BOND : bond 0.00314 / 0.17 ( 45) SS BOND : angle 1.38194 / 0.86 ( 90) hydrogen bonds : bond 0.02993 / 1.85 ( 204) hydrogen bonds : angle 6.10000 / 4.41 ( 501) link_ALPHA1-3 : bond 0.00549 / 0.38 ( 2) link_ALPHA1-3 : angle 1.43985 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00675 / 0.46 ( 2) link_ALPHA1-6 : angle 1.33244 / 0.89 ( 6) link_BETA1-4 : bond 0.00882 / 0.58 ( 4) link_BETA1-4 : angle 3.47624 / 1.68 ( 12) link_NAG-ASN : bond 0.01388 / 0.78 ( 10) link_NAG-ASN : angle 5.80127 / 3.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9275 (tpt) cc_final: 0.8883 (mmt) REVERT: A 4804 ARG cc_start: 0.8595 (tpm170) cc_final: 0.8381 (tpm170) REVERT: B 4411 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 4594 ASN cc_start: 0.8751 (t0) cc_final: 0.8445 (t0) outliers start: 19 outliers final: 14 residues processed: 41 average time/residue: 0.0568 time to fit residues: 3.6327 Evaluate side-chains 39 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4698 CYS Chi-restraints excluded: chain A residue 4738 ASN Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4411 LEU Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4729 THR Chi-restraints excluded: chain B residue 4791 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 46 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.096376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063873 restraints weight = 20970.794| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 5.05 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7316 Z= 0.160 Angle : 0.793 18.354 10050 Z= 0.364 Chirality : 0.054 0.573 1133 Planarity : 0.005 0.070 1282 Dihedral : 5.651 58.912 942 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.40 % Allowed : 18.18 % Favored : 79.42 % 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 are not related in a simple way. whole: -1.47 (0.29), residues: 872 helix: 3.01 (0.66), residues: 66 sheet: -0.62 (0.39), residues: 170 loop : -1.64 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B4488 TYR 0.011 0.001 TYR B4440 PHE 0.014 0.001 PHE B4674 TRP 0.019 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7253) covalent geometry : angle 0.71080 / 0.34 ( 9906) SS BOND : bond 0.00315 / 0.17 ( 45) SS BOND : angle 1.24361 / 0.76 ( 90) hydrogen bonds : bond 0.02975 / 1.84 ( 204) hydrogen bonds : angle 5.94050 / 4.31 ( 501) link_ALPHA1-3 : bond 0.00531 / 0.36 ( 2) link_ALPHA1-3 : angle 1.47630 / 1.00 ( 6) link_ALPHA1-6 : bond 0.00653 / 0.44 ( 2) link_ALPHA1-6 : angle 1.34524 / 0.90 ( 6) link_BETA1-4 : bond 0.00809 / 0.53 ( 4) link_BETA1-4 : angle 3.44881 / 1.70 ( 12) link_NAG-ASN : bond 0.01387 / 0.79 ( 10) link_NAG-ASN : angle 5.81228 / 3.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 26 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9290 (tpt) cc_final: 0.8887 (mmt) REVERT: B 4411 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 4594 ASN cc_start: 0.8725 (t0) cc_final: 0.8425 (t0) REVERT: B 4611 HIS cc_start: 0.8429 (p-80) cc_final: 0.8118 (p-80) outliers start: 19 outliers final: 14 residues processed: 42 average time/residue: 0.0461 time to fit residues: 3.0148 Evaluate side-chains 40 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4698 CYS Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4411 LEU Chi-restraints excluded: chain B residue 4459 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4554 LEU Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4791 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 11 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 33 optimal weight: 0.0030 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.097805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065739 restraints weight = 20722.740| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.98 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7316 Z= 0.131 Angle : 0.798 17.478 10050 Z= 0.364 Chirality : 0.056 0.563 1133 Planarity : 0.005 0.066 1282 Dihedral : 5.494 57.241 942 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.89 % Allowed : 18.81 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.29), residues: 872 helix: 2.98 (0.65), residues: 66 sheet: -0.61 (0.39), residues: 170 loop : -1.61 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4804 TYR 0.011 0.001 TYR B4440 PHE 0.005 0.001 PHE A4784 TRP 0.018 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7253) covalent geometry : angle 0.71300 / 0.34 ( 9906) SS BOND : bond 0.00260 / 0.13 ( 45) SS BOND : angle 1.11745 / 0.67 ( 90) hydrogen bonds : bond 0.02746 / 1.71 ( 204) hydrogen bonds : angle 5.76438 / 4.18 ( 501) link_ALPHA1-3 : bond 0.00532 / 0.37 ( 2) link_ALPHA1-3 : angle 1.40786 / 0.96 ( 6) link_ALPHA1-6 : bond 0.00678 / 0.46 ( 2) link_ALPHA1-6 : angle 1.30991 / 0.88 ( 6) link_BETA1-4 : bond 0.00762 / 0.50 ( 4) link_BETA1-4 : angle 3.35699 / 1.71 ( 12) link_NAG-ASN : bond 0.01513 / 0.89 ( 10) link_NAG-ASN : angle 6.06092 / 3.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9301 (tpt) cc_final: 0.8932 (mmt) REVERT: B 4594 ASN cc_start: 0.8681 (t0) cc_final: 0.8384 (t0) REVERT: B 4611 HIS cc_start: 0.8452 (p-80) cc_final: 0.8137 (p-80) outliers start: 15 outliers final: 15 residues processed: 41 average time/residue: 0.0565 time to fit residues: 3.6010 Evaluate side-chains 40 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4698 CYS Chi-restraints excluded: chain A residue 4738 ASN Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4459 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4554 LEU Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4791 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 41 optimal weight: 20.0000 chunk 65 optimal weight: 0.0030 chunk 52 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 0.0010 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.097270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064733 restraints weight = 20818.175| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 5.08 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7316 Z= 0.144 Angle : 0.817 18.654 10050 Z= 0.375 Chirality : 0.056 0.562 1133 Planarity : 0.005 0.070 1282 Dihedral : 5.495 56.846 942 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.40 % Allowed : 18.31 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.29), residues: 872 helix: 3.00 (0.65), residues: 66 sheet: -0.69 (0.38), residues: 182 loop : -1.58 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B4702 TYR 0.010 0.001 TYR B4440 PHE 0.018 0.001 PHE B4674 TRP 0.023 0.001 TRP A4376 HIS 0.004 0.000 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7253) covalent geometry : angle 0.72348 / 0.35 ( 9906) SS BOND : bond 0.00267 / 0.14 ( 45) SS BOND : angle 1.67887 / 1.40 ( 90) hydrogen bonds : bond 0.02834 / 1.77 ( 204) hydrogen bonds : angle 5.69955 / 4.14 ( 501) link_ALPHA1-3 : bond 0.00514 / 0.35 ( 2) link_ALPHA1-3 : angle 1.45209 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00693 / 0.47 ( 2) link_ALPHA1-6 : angle 1.34027 / 0.90 ( 6) link_BETA1-4 : bond 0.00790 / 0.52 ( 4) link_BETA1-4 : angle 3.33394 / 1.64 ( 12) link_NAG-ASN : bond 0.01613 / 0.96 ( 10) link_NAG-ASN : angle 6.09517 / 3.96 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 27 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9303 (tpt) cc_final: 0.8942 (mmt) REVERT: B 4594 ASN cc_start: 0.8709 (t0) cc_final: 0.8409 (t0) REVERT: B 4611 HIS cc_start: 0.8460 (p-80) cc_final: 0.8130 (p-80) outliers start: 19 outliers final: 18 residues processed: 43 average time/residue: 0.0522 time to fit residues: 3.5091 Evaluate side-chains 43 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4578 ASN Chi-restraints excluded: chain A residue 4698 CYS Chi-restraints excluded: chain A residue 4738 ASN Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4459 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4544 GLU Chi-restraints excluded: chain B residue 4554 LEU Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4729 THR Chi-restraints excluded: chain B residue 4786 CYS Chi-restraints excluded: chain B residue 4791 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.096864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064486 restraints weight = 20950.230| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 5.04 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7316 Z= 0.161 Angle : 0.803 18.499 10050 Z= 0.368 Chirality : 0.055 0.556 1133 Planarity : 0.005 0.065 1282 Dihedral : 5.516 56.718 942 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.40 % Allowed : 18.18 % Favored : 79.42 % 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 are not related in a simple way. whole: -1.40 (0.29), residues: 872 helix: 3.03 (0.65), residues: 66 sheet: -0.72 (0.38), residues: 182 loop : -1.55 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B4488 TYR 0.010 0.001 TYR A4440 PHE 0.015 0.001 PHE B4674 TRP 0.021 0.002 TRP A4376 HIS 0.003 0.000 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 7253) covalent geometry : angle 0.71778 / 0.35 ( 9906) SS BOND : bond 0.00297 / 0.16 ( 45) SS BOND : angle 1.21429 / 0.80 ( 90) hydrogen bonds : bond 0.02976 / 1.85 ( 204) hydrogen bonds : angle 5.69243 / 4.14 ( 501) link_ALPHA1-3 : bond 0.00495 / 0.34 ( 2) link_ALPHA1-3 : angle 1.45538 / 0.97 ( 6) link_ALPHA1-6 : bond 0.00622 / 0.42 ( 2) link_ALPHA1-6 : angle 1.39221 / 0.93 ( 6) link_BETA1-4 : bond 0.00852 / 0.57 ( 4) link_BETA1-4 : angle 3.31033 / 1.69 ( 12) link_NAG-ASN : bond 0.01580 / 0.94 ( 10) link_NAG-ASN : angle 6.00160 / 3.91 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.70 seconds wall clock time: 23 minutes 15.62 seconds (1395.62 seconds total)