Starting phenix.real_space_refine on Sat Apr 6 04:56:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcu_13899/04_2024/7qcu_13899.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcu_13899/04_2024/7qcu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcu_13899/04_2024/7qcu_13899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcu_13899/04_2024/7qcu_13899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcu_13899/04_2024/7qcu_13899.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcu_13899/04_2024/7qcu_13899.pdb" } 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 Residue "A PHE 4556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.78, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 3.10 Conformation dependent library (CDL) restraints added in 1.3 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: 0.88 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: 2.19 Time building geometry restraints manager: 3.38 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: 84.85 - 95.14: 7 95.14 - 105.43: 401 105.43 - 115.72: 4322 115.72 - 126.01: 5014 126.01 - 136.29: 162 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 2.440 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 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: 4.190 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: 16.950 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.620 Find NCS groups from input model: 0.420 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.330 ------------------------------------------------------------------------------- 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 0.195 7253 Z= 0.848 Angle : 2.179 25.386 9906 Z= 1.450 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 *********************** 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 fitting. rotamer outliers: 55 poor density : 66 time to evaluate : 0.860 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: 0.1835 time to fit residues: 29.1054 Evaluate side-chains 41 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 28 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 0.6980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4686 GLN A4839 ASN B4425 HIS B4439 HIS ** B4505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4533 GLN ** B4801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 7253 Z= 0.275 Angle : 0.875 12.146 9906 Z= 0.430 Chirality : 0.057 0.358 1133 Planarity : 0.006 0.058 1282 Dihedral : 18.978 112.684 1323 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 3.41 % Allowed : 12.50 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.54 (0.28), residues: 872 helix: 1.94 (0.65), residues: 66 sheet: -0.62 (0.38), residues: 173 loop : -1.58 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A4376 HIS 0.007 0.001 HIS B4505 PHE 0.022 0.002 PHE B4674 TYR 0.021 0.001 TYR B4527 ARG 0.006 0.001 ARG A4564 *********************** 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 fitting. rotamer outliers: 27 poor density : 32 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 59 average time/residue: 0.1457 time to fit residues: 13.0898 Evaluate side-chains 34 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 23 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.0030 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4505 HIS ** A4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7253 Z= 0.264 Angle : 0.796 10.282 9906 Z= 0.384 Chirality : 0.054 0.595 1133 Planarity : 0.005 0.056 1282 Dihedral : 16.391 111.636 1312 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.16 % Allowed : 14.65 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.40 (0.29), residues: 872 helix: 2.63 (0.66), residues: 66 sheet: -0.42 (0.38), residues: 185 loop : -1.60 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A4377 HIS 0.007 0.001 HIS B4611 PHE 0.015 0.001 PHE B4674 TYR 0.012 0.001 TYR B4440 ARG 0.004 0.001 ARG A4564 *********************** 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 55 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 30 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 54 average time/residue: 0.1467 time to fit residues: 12.0848 Evaluate side-chains 38 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 22 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4737 GLN 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 4729 THR 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 4832 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4512 GLN ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7253 Z= 0.233 Angle : 0.735 8.881 9906 Z= 0.357 Chirality : 0.052 0.343 1133 Planarity : 0.005 0.061 1282 Dihedral : 15.243 115.407 1309 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.03 % Allowed : 15.66 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 2.87 (0.67), residues: 66 sheet: -0.49 (0.39), residues: 175 loop : -1.58 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4376 HIS 0.006 0.001 HIS B4505 PHE 0.012 0.001 PHE B4674 TYR 0.010 0.001 TYR B4440 ARG 0.003 0.000 ARG A4564 *********************** 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 52 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 28 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4768 CYS cc_start: 0.5670 (OUTLIER) cc_final: 0.5361 (p) outliers start: 24 outliers final: 14 residues processed: 47 average time/residue: 0.1451 time to fit residues: 10.7309 Evaluate side-chains 39 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 24 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4824 VAL Chi-restraints excluded: chain B residue 4395 VAL Chi-restraints excluded: chain B residue 4498 GLU Chi-restraints excluded: chain B residue 4522 LEU 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 4768 CYS Chi-restraints excluded: chain B residue 4786 CYS Chi-restraints excluded: chain B residue 4791 CYS Chi-restraints excluded: chain B residue 4832 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4512 GLN A4737 GLN ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7253 Z= 0.355 Angle : 0.770 9.610 9906 Z= 0.373 Chirality : 0.055 0.621 1133 Planarity : 0.005 0.064 1282 Dihedral : 14.980 115.569 1309 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.54 % Allowed : 16.04 % Favored : 80.43 % 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: 2.96 (0.67), residues: 66 sheet: -0.54 (0.37), residues: 185 loop : -1.62 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4424 HIS 0.004 0.001 HIS B4611 PHE 0.012 0.002 PHE B4469 TYR 0.012 0.001 TYR B4524 ARG 0.003 0.001 ARG A4702 *********************** 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 53 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 25 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4768 CYS cc_start: 0.5634 (OUTLIER) cc_final: 0.5390 (p) outliers start: 28 outliers final: 21 residues processed: 49 average time/residue: 0.1474 time to fit residues: 11.2530 Evaluate side-chains 45 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 23 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4395 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 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4383 MET 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 4768 CYS 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 4832 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7253 Z= 0.231 Angle : 0.744 9.916 9906 Z= 0.356 Chirality : 0.051 0.323 1133 Planarity : 0.005 0.065 1282 Dihedral : 13.697 107.907 1309 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.90 % Allowed : 17.05 % 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: -1.47 (0.29), residues: 872 helix: 2.94 (0.67), residues: 66 sheet: -0.61 (0.38), residues: 175 loop : -1.64 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 PHE 0.008 0.001 PHE B4469 TYR 0.010 0.001 TYR A4440 ARG 0.002 0.000 ARG A4564 *********************** 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 48 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 25 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4768 CYS cc_start: 0.5418 (OUTLIER) cc_final: 0.5024 (p) outliers start: 23 outliers final: 18 residues processed: 44 average time/residue: 0.1570 time to fit residues: 10.7342 Evaluate side-chains 42 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 23 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4395 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 4383 MET Chi-restraints excluded: chain B residue 4395 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 4675 MET Chi-restraints excluded: chain B residue 4729 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 4832 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7253 Z= 0.223 Angle : 0.720 9.034 9906 Z= 0.342 Chirality : 0.050 0.329 1133 Planarity : 0.005 0.062 1282 Dihedral : 13.169 105.720 1308 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.28 % Allowed : 17.55 % 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: -1.42 (0.29), residues: 872 helix: 2.96 (0.66), residues: 66 sheet: -0.57 (0.38), residues: 175 loop : -1.61 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A4376 HIS 0.004 0.001 HIS B4611 PHE 0.015 0.001 PHE B4674 TYR 0.009 0.001 TYR A4440 ARG 0.002 0.000 ARG A4564 *********************** 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 54 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 28 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 24 residues processed: 49 average time/residue: 0.1647 time to fit residues: 12.5600 Evaluate side-chains 48 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 24 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4395 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 4383 MET Chi-restraints excluded: chain B residue 4395 VAL Chi-restraints excluded: chain B residue 4459 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4489 THR 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 4577 THR Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4729 THR Chi-restraints excluded: chain B residue 4768 CYS 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 4832 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** ** B4611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4825 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7253 Z= 0.236 Angle : 0.730 8.882 9906 Z= 0.346 Chirality : 0.050 0.327 1133 Planarity : 0.005 0.068 1282 Dihedral : 12.717 102.752 1308 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.16 % Allowed : 17.93 % 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: -1.34 (0.29), residues: 872 helix: 2.97 (0.66), residues: 66 sheet: -0.52 (0.38), residues: 175 loop : -1.53 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A4376 HIS 0.008 0.001 HIS B4611 PHE 0.008 0.001 PHE B4469 TYR 0.010 0.001 TYR A4440 ARG 0.002 0.000 ARG A4564 *********************** 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 53 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 28 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 20 residues processed: 48 average time/residue: 0.1522 time to fit residues: 11.2814 Evaluate side-chains 45 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 25 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4395 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 4383 MET 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 4729 THR Chi-restraints excluded: chain B residue 4768 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.0170 chunk 51 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4512 GLN ** B4611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7253 Z= 0.207 Angle : 0.725 10.176 9906 Z= 0.342 Chirality : 0.051 0.327 1133 Planarity : 0.005 0.060 1282 Dihedral : 12.565 102.437 1308 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.41 % Allowed : 17.55 % 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: -1.31 (0.29), residues: 872 helix: 2.95 (0.66), residues: 66 sheet: -0.45 (0.38), residues: 175 loop : -1.53 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4376 HIS 0.006 0.001 HIS B4611 PHE 0.013 0.001 PHE B4674 TYR 0.009 0.001 TYR A4440 ARG 0.002 0.000 ARG A4564 *********************** 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 55 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 28 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 21 residues processed: 50 average time/residue: 0.1458 time to fit residues: 11.3729 Evaluate side-chains 48 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 27 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4392 VAL Chi-restraints excluded: chain A residue 4395 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 4383 MET Chi-restraints excluded: chain B residue 4459 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4489 THR 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 4768 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 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B4611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7253 Z= 0.239 Angle : 0.734 9.080 9906 Z= 0.349 Chirality : 0.051 0.361 1133 Planarity : 0.005 0.062 1282 Dihedral : 12.242 99.604 1308 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.90 % Allowed : 18.06 % 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: -1.25 (0.29), residues: 872 helix: 3.01 (0.66), residues: 66 sheet: -0.40 (0.38), residues: 175 loop : -1.49 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4426 HIS 0.005 0.001 HIS B4611 PHE 0.008 0.001 PHE B4469 TYR 0.010 0.001 TYR A4440 ARG 0.002 0.000 ARG A4564 ********************** 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 53 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 30 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 22 residues processed: 48 average time/residue: 0.1557 time to fit residues: 11.5236 Evaluate side-chains 48 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 26 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 4768 CYS Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4824 VAL Chi-restraints excluded: chain B residue 4383 MET Chi-restraints excluded: chain B residue 4395 VAL Chi-restraints excluded: chain B residue 4459 VAL Chi-restraints excluded: chain B residue 4463 SER Chi-restraints excluded: chain B residue 4489 THR 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 4729 THR Chi-restraints excluded: chain B residue 4768 CYS 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 21 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4512 GLN ** B4611 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.095866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064536 restraints weight = 20571.986| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.84 r_work: 0.3060 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7253 Z= 0.245 Angle : 0.746 10.770 9906 Z= 0.354 Chirality : 0.051 0.324 1133 Planarity : 0.005 0.060 1282 Dihedral : 12.100 98.340 1308 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.28 % Allowed : 18.06 % Favored : 78.66 % 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: -1.20 (0.29), residues: 872 helix: 3.02 (0.66), residues: 66 sheet: -0.39 (0.38), residues: 175 loop : -1.45 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4426 HIS 0.005 0.001 HIS B4611 PHE 0.014 0.001 PHE B4674 TYR 0.010 0.001 TYR A4440 ARG 0.002 0.000 ARG A4564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1894.77 seconds wall clock time: 35 minutes 19.33 seconds (2119.33 seconds total)