Starting phenix.real_space_refine on Fri Jun 6 07:30:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qcu_13899/06_2025/7qcu_13899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qcu_13899/06_2025/7qcu_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_13899/06_2025/7qcu_13899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qcu_13899/06_2025/7qcu_13899.map" model { file = "/net/cci-nas-00/data/ceres_data/7qcu_13899/06_2025/7qcu_13899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qcu_13899/06_2025/7qcu_13899.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.12, per 1000 atoms: 1.01 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: 3.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.86 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: 2.69 Time building geometry restraints manager: 3.80 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 - 24.82: 4255 24.82 - 49.64: 312 49.64 - 74.47: 53 74.47 - 99.29: 47 99.29 - 124.11: 20 Dihedral angle restraints: 4687 sinusoidal: 2101 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 4684 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: 33.670 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 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 : 20.445 124.108 2888 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (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 TRP 0.034 0.005 TRP B4602 HIS 0.012 0.002 HIS B4505 PHE 0.040 0.003 PHE B4782 TYR 0.065 0.004 TYR A4532 ARG 0.021 0.002 ARG B4488 Details of bonding type rmsd link_NAG-ASN : bond 0.01484 ( 10) link_NAG-ASN : angle 8.22724 ( 30) link_ALPHA1-6 : bond 0.00241 ( 2) link_ALPHA1-6 : angle 0.75745 ( 6) link_BETA1-4 : bond 0.02405 ( 4) link_BETA1-4 : angle 7.43137 ( 12) link_ALPHA1-3 : bond 0.00085 ( 2) link_ALPHA1-3 : angle 0.53672 ( 6) hydrogen bonds : bond 0.18183 ( 204) hydrogen bonds : angle 9.86054 ( 501) SS BOND : bond 0.04390 ( 45) SS BOND : angle 5.17592 ( 90) covalent geometry : bond 0.01267 ( 7253) covalent geometry : angle 2.17907 ( 9906) *********************** 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 : 0.820 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: 0.2191 time to fit residues: 36.3429 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 : 0.718 ------------------------------------------------------------------------------- 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 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** B4686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.103993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071948 restraints weight = 20318.661| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.94 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7316 Z= 0.197 Angle : 0.989 15.500 10050 Z= 0.465 Chirality : 0.058 0.343 1133 Planarity : 0.006 0.057 1282 Dihedral : 18.736 113.452 1323 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 3.54 % Allowed : 12.25 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.28), residues: 872 helix: 1.98 (0.65), residues: 66 sheet: -0.56 (0.38), residues: 171 loop : -1.64 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A4376 HIS 0.007 0.001 HIS B4611 PHE 0.022 0.002 PHE B4674 TYR 0.023 0.001 TYR B4527 ARG 0.005 0.001 ARG A4564 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 10) link_NAG-ASN : angle 5.47295 ( 30) link_ALPHA1-6 : bond 0.00770 ( 2) link_ALPHA1-6 : angle 1.50453 ( 6) link_BETA1-4 : bond 0.00987 ( 4) link_BETA1-4 : angle 5.19308 ( 12) link_ALPHA1-3 : bond 0.00680 ( 2) link_ALPHA1-3 : angle 2.32325 ( 6) hydrogen bonds : bond 0.04116 ( 204) hydrogen bonds : angle 7.59161 ( 501) SS BOND : bond 0.00400 ( 45) SS BOND : angle 2.02560 ( 90) covalent geometry : bond 0.00428 ( 7253) covalent geometry : angle 0.90966 ( 9906) *********************** 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 59 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8994 (mmm) REVERT: A 4428 CYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7189 (p) REVERT: A 4478 CYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6677 (p) REVERT: A 4509 MET cc_start: 0.8790 (ptm) cc_final: 0.8516 (ptp) REVERT: A 4578 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8041 (t0) REVERT: B 4376 TRP cc_start: 0.8616 (m100) cc_final: 0.8253 (m100) outliers start: 28 outliers final: 11 residues processed: 58 average time/residue: 0.1436 time to fit residues: 12.9040 Evaluate side-chains 37 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 4786 CYS 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 79 optimal weight: 0.8980 chunk 70 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4801 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 = 0.3902 r_free = 0.3902 target = 0.096995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064657 restraints weight = 20558.224| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 5.00 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7316 Z= 0.177 Angle : 0.924 19.521 10050 Z= 0.418 Chirality : 0.057 0.744 1133 Planarity : 0.005 0.057 1282 Dihedral : 16.041 114.070 1315 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.03 % Allowed : 14.52 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.28), residues: 872 helix: 2.61 (0.65), residues: 66 sheet: -0.54 (0.40), residues: 165 loop : -1.64 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A4377 HIS 0.006 0.001 HIS B4611 PHE 0.016 0.001 PHE B4674 TYR 0.015 0.001 TYR B4440 ARG 0.004 0.001 ARG A4564 Details of bonding type rmsd link_NAG-ASN : bond 0.01746 ( 10) link_NAG-ASN : angle 7.00777 ( 30) link_ALPHA1-6 : bond 0.00736 ( 2) link_ALPHA1-6 : angle 1.52997 ( 6) link_BETA1-4 : bond 0.00718 ( 4) link_BETA1-4 : angle 4.64853 ( 12) link_ALPHA1-3 : bond 0.01041 ( 2) link_ALPHA1-3 : angle 1.42622 ( 6) hydrogen bonds : bond 0.03411 ( 204) hydrogen bonds : angle 6.95784 ( 501) SS BOND : bond 0.00365 ( 45) SS BOND : angle 1.21711 ( 90) covalent geometry : bond 0.00385 ( 7253) covalent geometry : angle 0.82166 ( 9906) *********************** 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 56 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 32 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4478 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6719 (p) REVERT: A 4509 MET cc_start: 0.8756 (ptm) cc_final: 0.8517 (ptp) REVERT: B 4376 TRP cc_start: 0.8507 (m100) cc_final: 0.8184 (m100) outliers start: 24 outliers final: 15 residues processed: 54 average time/residue: 0.1386 time to fit residues: 11.8090 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 : 0.772 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4505 HIS ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4801 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.096214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.063901 restraints weight = 21019.718| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 5.04 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7316 Z= 0.172 Angle : 0.835 18.042 10050 Z= 0.384 Chirality : 0.053 0.422 1133 Planarity : 0.005 0.059 1282 Dihedral : 15.188 117.047 1313 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.41 % Allowed : 14.90 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.28), residues: 872 helix: 2.87 (0.67), residues: 66 sheet: -0.38 (0.39), residues: 180 loop : -1.70 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A4376 HIS 0.005 0.001 HIS B4505 PHE 0.012 0.001 PHE B4674 TYR 0.013 0.001 TYR B4440 ARG 0.003 0.000 ARG A4564 Details of bonding type rmsd link_NAG-ASN : bond 0.01533 ( 10) link_NAG-ASN : angle 5.89176 ( 30) link_ALPHA1-6 : bond 0.00695 ( 2) link_ALPHA1-6 : angle 1.65471 ( 6) link_BETA1-4 : bond 0.00576 ( 4) link_BETA1-4 : angle 4.64956 ( 12) link_ALPHA1-3 : bond 0.01191 ( 2) link_ALPHA1-3 : angle 1.51270 ( 6) hydrogen bonds : bond 0.03211 ( 204) hydrogen bonds : angle 6.63422 ( 501) SS BOND : bond 0.00317 ( 45) SS BOND : angle 1.22767 ( 90) covalent geometry : bond 0.00380 ( 7253) covalent geometry : angle 0.74820 ( 9906) *********************** 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 54 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 27 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4478 CYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6786 (p) REVERT: A 4509 MET cc_start: 0.8721 (ptm) cc_final: 0.8503 (ptp) REVERT: B 4376 TRP cc_start: 0.8450 (m100) cc_final: 0.8072 (m100) REVERT: B 4729 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8381 (t) outliers start: 27 outliers final: 14 residues processed: 49 average time/residue: 0.1365 time to fit residues: 10.6144 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 : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3879 r_free = 0.3879 target = 0.095611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.063333 restraints weight = 20684.449| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.99 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7316 Z= 0.190 Angle : 0.830 18.303 10050 Z= 0.382 Chirality : 0.053 0.342 1133 Planarity : 0.005 0.060 1282 Dihedral : 14.524 113.667 1309 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.90 % Allowed : 16.29 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.28), residues: 872 helix: 3.00 (0.67), residues: 66 sheet: -0.51 (0.38), residues: 185 loop : -1.75 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 PHE 0.011 0.001 PHE B4674 TYR 0.011 0.001 TYR B4440 ARG 0.002 0.000 ARG A4564 Details of bonding type rmsd link_NAG-ASN : bond 0.01356 ( 10) link_NAG-ASN : angle 5.71069 ( 30) link_ALPHA1-6 : bond 0.00587 ( 2) link_ALPHA1-6 : angle 1.82264 ( 6) link_BETA1-4 : bond 0.00606 ( 4) link_BETA1-4 : angle 4.60638 ( 12) link_ALPHA1-3 : bond 0.01209 ( 2) link_ALPHA1-3 : angle 1.25016 ( 6) hydrogen bonds : bond 0.03221 ( 204) hydrogen bonds : angle 6.41071 ( 501) SS BOND : bond 0.00309 ( 45) SS BOND : angle 1.17305 ( 90) covalent geometry : bond 0.00424 ( 7253) covalent geometry : angle 0.74742 ( 9906) *********************** 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 54 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4509 MET cc_start: 0.8738 (ptm) cc_final: 0.8529 (ptp) outliers start: 23 outliers final: 18 residues processed: 49 average time/residue: 0.1382 time to fit residues: 10.7036 Evaluate side-chains 41 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 23 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 4577 THR 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 4790 VAL 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 2 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3892 r_free = 0.3892 target = 0.096385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064002 restraints weight = 20754.224| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 5.03 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3387 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= 0.152 Angle : 0.818 18.236 10050 Z= 0.375 Chirality : 0.053 0.345 1133 Planarity : 0.005 0.061 1282 Dihedral : 14.184 112.303 1309 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.65 % Allowed : 17.30 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 872 helix: 2.97 (0.66), residues: 66 sheet: -0.57 (0.39), residues: 170 loop : -1.71 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 PHE 0.019 0.001 PHE B4674 TYR 0.011 0.001 TYR B4440 ARG 0.003 0.000 ARG A4564 Details of bonding type rmsd link_NAG-ASN : bond 0.01350 ( 10) link_NAG-ASN : angle 5.57420 ( 30) link_ALPHA1-6 : bond 0.00550 ( 2) link_ALPHA1-6 : angle 1.85901 ( 6) link_BETA1-4 : bond 0.00587 ( 4) link_BETA1-4 : angle 4.67161 ( 12) link_ALPHA1-3 : bond 0.01234 ( 2) link_ALPHA1-3 : angle 1.13518 ( 6) hydrogen bonds : bond 0.02976 ( 204) hydrogen bonds : angle 6.17345 ( 501) SS BOND : bond 0.00285 ( 45) SS BOND : angle 1.27311 ( 90) covalent geometry : bond 0.00338 ( 7253) covalent geometry : angle 0.73574 ( 9906) *********************** 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 49 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 28 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4594 ASN cc_start: 0.8755 (t0) cc_final: 0.8476 (t0) outliers start: 21 outliers final: 17 residues processed: 45 average time/residue: 0.1385 time to fit residues: 9.8765 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 : 0.728 ------------------------------------------------------------------------------- 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 4577 THR Chi-restraints excluded: chain B residue 4675 MET 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 43 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3891 r_free = 0.3891 target = 0.096576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.063967 restraints weight = 20729.567| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 5.07 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3564 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= 0.148 Angle : 0.828 18.322 10050 Z= 0.376 Chirality : 0.053 0.349 1133 Planarity : 0.005 0.062 1282 Dihedral : 13.928 110.495 1308 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.78 % Allowed : 17.42 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.28), residues: 872 helix: 2.97 (0.66), residues: 66 sheet: -0.55 (0.39), residues: 170 loop : -1.70 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4376 HIS 0.004 0.000 HIS B4611 PHE 0.015 0.001 PHE B4674 TYR 0.011 0.001 TYR B4440 ARG 0.002 0.000 ARG A4564 Details of bonding type rmsd link_NAG-ASN : bond 0.01339 ( 10) link_NAG-ASN : angle 5.57304 ( 30) link_ALPHA1-6 : bond 0.00515 ( 2) link_ALPHA1-6 : angle 1.82416 ( 6) link_BETA1-4 : bond 0.00674 ( 4) link_BETA1-4 : angle 4.61645 ( 12) link_ALPHA1-3 : bond 0.01219 ( 2) link_ALPHA1-3 : angle 1.10996 ( 6) hydrogen bonds : bond 0.02938 ( 204) hydrogen bonds : angle 6.02769 ( 501) SS BOND : bond 0.00274 ( 45) SS BOND : angle 1.31552 ( 90) covalent geometry : bond 0.00333 ( 7253) covalent geometry : angle 0.74667 ( 9906) *********************** 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 51 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4411 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8302 (mp) REVERT: B 4512 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: B 4594 ASN cc_start: 0.8740 (t0) cc_final: 0.8467 (t0) REVERT: B 4611 HIS cc_start: 0.8448 (p-80) cc_final: 0.8152 (p-80) outliers start: 22 outliers final: 16 residues processed: 46 average time/residue: 0.1763 time to fit residues: 12.3354 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 : 0.866 ------------------------------------------------------------------------------- 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 4459 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 4577 THR Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4790 VAL 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 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 42 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4477 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.095326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062667 restraints weight = 20917.079| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 5.04 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7316 Z= 0.201 Angle : 0.839 18.285 10050 Z= 0.383 Chirality : 0.053 0.350 1133 Planarity : 0.005 0.068 1282 Dihedral : 13.695 108.120 1308 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.40 % Allowed : 18.43 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.29), residues: 872 helix: 3.03 (0.66), residues: 66 sheet: -0.73 (0.38), residues: 182 loop : -1.66 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 PHE 0.009 0.001 PHE B4469 TYR 0.010 0.001 TYR B4440 ARG 0.003 0.000 ARG B4488 Details of bonding type rmsd link_NAG-ASN : bond 0.01302 ( 10) link_NAG-ASN : angle 5.55051 ( 30) link_ALPHA1-6 : bond 0.00505 ( 2) link_ALPHA1-6 : angle 1.86677 ( 6) link_BETA1-4 : bond 0.00664 ( 4) link_BETA1-4 : angle 4.58632 ( 12) link_ALPHA1-3 : bond 0.01140 ( 2) link_ALPHA1-3 : angle 1.11402 ( 6) hydrogen bonds : bond 0.03131 ( 204) hydrogen bonds : angle 6.00013 ( 501) SS BOND : bond 0.00357 ( 45) SS BOND : angle 1.33925 ( 90) covalent geometry : bond 0.00452 ( 7253) covalent geometry : angle 0.75913 ( 9906) *********************** 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 46 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 27 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4411 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 4594 ASN cc_start: 0.8708 (t0) cc_final: 0.8404 (t0) REVERT: B 4611 HIS cc_start: 0.8420 (p-80) cc_final: 0.8111 (p-80) outliers start: 19 outliers final: 17 residues processed: 42 average time/residue: 0.1495 time to fit residues: 9.8354 Evaluate side-chains 42 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 4577 THR Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4791 CYS Chi-restraints excluded: chain B residue 4798 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 72 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4477 HIS ** 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 = 0.3910 r_free = 0.3910 target = 0.096816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.064613 restraints weight = 21265.708| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 5.03 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7316 Z= 0.146 Angle : 0.837 18.291 10050 Z= 0.376 Chirality : 0.053 0.351 1133 Planarity : 0.005 0.070 1282 Dihedral : 13.336 108.906 1308 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.40 % Allowed : 18.56 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.29), residues: 872 helix: 3.04 (0.65), residues: 66 sheet: -0.67 (0.38), residues: 182 loop : -1.61 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4426 HIS 0.003 0.000 HIS B4611 PHE 0.015 0.001 PHE B4674 TYR 0.011 0.001 TYR B4440 ARG 0.002 0.000 ARG B4488 Details of bonding type rmsd link_NAG-ASN : bond 0.01418 ( 10) link_NAG-ASN : angle 5.78258 ( 30) link_ALPHA1-6 : bond 0.00452 ( 2) link_ALPHA1-6 : angle 1.84190 ( 6) link_BETA1-4 : bond 0.00690 ( 4) link_BETA1-4 : angle 4.76631 ( 12) link_ALPHA1-3 : bond 0.01157 ( 2) link_ALPHA1-3 : angle 1.04559 ( 6) hydrogen bonds : bond 0.02835 ( 204) hydrogen bonds : angle 5.82037 ( 501) SS BOND : bond 0.00247 ( 45) SS BOND : angle 1.16354 ( 90) covalent geometry : bond 0.00327 ( 7253) covalent geometry : angle 0.75240 ( 9906) *********************** 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 46 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 27 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4594 ASN cc_start: 0.8686 (t0) cc_final: 0.8410 (t0) REVERT: B 4611 HIS cc_start: 0.8450 (p-80) cc_final: 0.8136 (p-80) outliers start: 19 outliers final: 17 residues processed: 42 average time/residue: 0.1593 time to fit residues: 10.5394 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 : 0.785 ------------------------------------------------------------------------------- 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 4544 GLU Chi-restraints excluded: chain B residue 4577 THR Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4791 CYS Chi-restraints excluded: chain B residue 4798 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 47 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4477 HIS ** 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 = 0.3888 r_free = 0.3888 target = 0.096297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.063545 restraints weight = 21511.595| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 5.13 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7316 Z= 0.152 Angle : 0.862 18.363 10050 Z= 0.391 Chirality : 0.053 0.354 1133 Planarity : 0.005 0.070 1282 Dihedral : 13.181 107.326 1308 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.53 % Allowed : 18.56 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.29), residues: 872 helix: 3.04 (0.65), residues: 66 sheet: -0.67 (0.38), residues: 182 loop : -1.55 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4426 HIS 0.003 0.000 HIS B4611 PHE 0.016 0.001 PHE B4674 TYR 0.010 0.001 TYR B4440 ARG 0.002 0.000 ARG B4488 Details of bonding type rmsd link_NAG-ASN : bond 0.01461 ( 10) link_NAG-ASN : angle 5.84388 ( 30) link_ALPHA1-6 : bond 0.00472 ( 2) link_ALPHA1-6 : angle 1.80291 ( 6) link_BETA1-4 : bond 0.00739 ( 4) link_BETA1-4 : angle 4.69741 ( 12) link_ALPHA1-3 : bond 0.01099 ( 2) link_ALPHA1-3 : angle 1.08606 ( 6) hydrogen bonds : bond 0.02910 ( 204) hydrogen bonds : angle 5.75956 ( 501) SS BOND : bond 0.00271 ( 45) SS BOND : angle 1.97205 ( 90) covalent geometry : bond 0.00339 ( 7253) covalent geometry : angle 0.76519 ( 9906) ********************** 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 48 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4594 ASN cc_start: 0.8707 (t0) cc_final: 0.8414 (t0) REVERT: B 4611 HIS cc_start: 0.8461 (p-80) cc_final: 0.8129 (p-80) outliers start: 20 outliers final: 17 residues processed: 45 average time/residue: 0.1409 time to fit residues: 9.9163 Evaluate side-chains 43 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 4544 GLU Chi-restraints excluded: chain B residue 4577 THR Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4786 CYS Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4791 CYS Chi-restraints excluded: chain B residue 4798 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 73 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4477 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.096635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064257 restraints weight = 21015.997| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 5.05 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7316 Z= 0.148 Angle : 0.847 18.339 10050 Z= 0.382 Chirality : 0.053 0.352 1133 Planarity : 0.005 0.067 1282 Dihedral : 12.861 105.703 1308 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.40 % Allowed : 18.56 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.29), residues: 872 helix: 3.06 (0.65), residues: 66 sheet: -0.74 (0.38), residues: 177 loop : -1.56 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4426 HIS 0.003 0.000 HIS B4611 PHE 0.016 0.001 PHE B4674 TYR 0.010 0.001 TYR B4440 ARG 0.003 0.000 ARG B4488 Details of bonding type rmsd link_NAG-ASN : bond 0.01499 ( 10) link_NAG-ASN : angle 5.90508 ( 30) link_ALPHA1-6 : bond 0.00429 ( 2) link_ALPHA1-6 : angle 1.84846 ( 6) link_BETA1-4 : bond 0.00738 ( 4) link_BETA1-4 : angle 4.86093 ( 12) link_ALPHA1-3 : bond 0.01082 ( 2) link_ALPHA1-3 : angle 1.07308 ( 6) hydrogen bonds : bond 0.02943 ( 204) hydrogen bonds : angle 5.69278 ( 501) SS BOND : bond 0.00247 ( 45) SS BOND : angle 1.35699 ( 90) covalent geometry : bond 0.00334 ( 7253) covalent geometry : angle 0.75784 ( 9906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3605.34 seconds wall clock time: 63 minutes 4.94 seconds (3784.94 seconds total)