Starting phenix.real_space_refine on Thu Jul 2 04:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.map" model { file = "/net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qcn_13897/07_2026/7qcn_13897.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.009 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 90 5.16 5 C 4012 2.51 5 N 1030 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6416 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3104 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3104 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6416 At special positions: 0 Unit cell: (93.74, 112.66, 104.06, 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 90 16.00 O 1282 8.00 N 1030 7.00 C 4012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A4363 " - pdb=" SG CYS A4386 " distance=2.03 Simple disulfide: pdb=" SG CYS A4379 " - pdb=" SG CYS B4379 " distance=2.09 Simple disulfide: pdb=" SG CYS A4381 " - pdb=" SG CYS A4422 " distance=2.03 Simple disulfide: pdb=" SG CYS A4399 " - pdb=" SG CYS A4423 " distance=2.03 Simple disulfide: pdb=" SG CYS A4407 " - pdb=" SG CYS A4428 " distance=2.05 Simple disulfide: pdb=" SG CYS A4430 " - pdb=" SG CYS A4576 " distance=2.03 Simple disulfide: pdb=" SG CYS A4432 " - pdb=" SG CYS A4573 " distance=2.03 Simple disulfide: pdb=" SG CYS A4454 " - pdb=" SG CYS A4612 " distance=2.02 Simple disulfide: pdb=" SG CYS A4478 " - pdb=" SG CYS A4486 " distance=2.04 Simple disulfide: pdb=" SG CYS A4584 " - pdb=" SG CYS A4595 " distance=2.02 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=1.99 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=2.02 Simple disulfide: pdb=" SG CYS A4748 " - pdb=" SG CYS A4762 " distance=2.03 Simple disulfide: pdb=" SG CYS A4768 " - pdb=" SG CYS A4791 " distance=2.04 Simple disulfide: pdb=" SG CYS A4789 " - pdb=" SG CYS A4800 " distance=2.04 Simple disulfide: pdb=" SG CYS B4363 " - pdb=" SG CYS B4386 " distance=2.03 Simple disulfide: pdb=" SG CYS B4381 " - pdb=" SG CYS B4422 " distance=2.03 Simple disulfide: pdb=" SG CYS B4399 " - pdb=" SG CYS B4423 " distance=2.03 Simple disulfide: pdb=" SG CYS B4407 " - pdb=" SG CYS B4428 " distance=2.05 Simple disulfide: pdb=" SG CYS B4430 " - pdb=" SG CYS B4576 " distance=2.03 Simple disulfide: pdb=" SG CYS B4432 " - pdb=" SG CYS B4573 " distance=2.03 Simple disulfide: pdb=" SG CYS B4454 " - pdb=" SG CYS B4612 " distance=2.02 Simple disulfide: pdb=" SG CYS B4478 " - pdb=" SG CYS B4486 " distance=2.04 Simple disulfide: pdb=" SG CYS B4584 " - pdb=" SG CYS B4595 " distance=2.02 Simple disulfide: pdb=" SG CYS B4638 " - pdb=" SG CYS B4673 " distance=2.03 Simple disulfide: pdb=" SG CYS B4644 " - pdb=" SG CYS B4668 " distance=2.03 Simple disulfide: pdb=" SG CYS B4655 " - pdb=" SG CYS B4692 " distance=1.99 Simple disulfide: pdb=" SG CYS B4682 " - pdb=" SG CYS B4709 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B4748 " - pdb=" SG CYS B4762 " distance=2.03 Simple disulfide: pdb=" SG CYS B4768 " - pdb=" SG CYS B4791 " distance=2.04 Simple disulfide: pdb=" SG CYS B4789 " - pdb=" SG CYS B4800 " distance=2.04 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 A5203 " - " ASN A4703 " " NAG A5204 " - " ASN A4738 " " NAG B5203 " - " ASN B4703 " " NAG B5204 " - " ASN B4738 " " NAG C 1 " - " ASN A4578 " " NAG D 1 " - " ASN B4578 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 486.1 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 15 sheets defined 15.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 4594 through 4599 removed outlier: 3.663A pdb=" N ALA A4598 " --> pdb=" O ASN A4594 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A4599 " --> pdb=" O CYS A4595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4594 through 4599' Processing helix chain 'A' and resid 4600 through 4602 No H-bonds generated for 'chain 'A' and resid 4600 through 4602' Processing helix chain 'A' and resid 4641 through 4646 Processing helix chain 'A' and resid 4647 through 4649 No H-bonds generated for 'chain 'A' and resid 4647 through 4649' Processing helix chain 'A' and resid 4651 through 4655 removed outlier: 4.212A pdb=" N GLN A4654 " --> pdb=" O LEU A4651 " (cutoff:3.500A) Processing helix chain 'A' and resid 4661 through 4675 removed outlier: 3.908A pdb=" N MET A4675 " --> pdb=" O ASP A4671 " (cutoff:3.500A) Processing helix chain 'A' and resid 4683 through 4695 removed outlier: 3.539A pdb=" N GLN A4695 " --> pdb=" O LEU A4691 " (cutoff:3.500A) Processing helix chain 'A' and resid 4701 through 4706 removed outlier: 4.140A pdb=" N HIS A4706 " --> pdb=" O ASN A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4737 removed outlier: 4.374A pdb=" N GLN A4737 " --> pdb=" O SER A4734 " (cutoff:3.500A) Processing helix chain 'B' and resid 4594 through 4599 removed outlier: 3.663A pdb=" N ALA B4598 " --> pdb=" O ASN B4594 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B4599 " --> pdb=" O CYS B4595 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4594 through 4599' Processing helix chain 'B' and resid 4600 through 4602 No H-bonds generated for 'chain 'B' and resid 4600 through 4602' Processing helix chain 'B' and resid 4641 through 4646 Processing helix chain 'B' and resid 4647 through 4649 No H-bonds generated for 'chain 'B' and resid 4647 through 4649' Processing helix chain 'B' and resid 4651 through 4655 removed outlier: 4.212A pdb=" N GLN B4654 " --> pdb=" O LEU B4651 " (cutoff:3.500A) Processing helix chain 'B' and resid 4661 through 4675 removed outlier: 3.908A pdb=" N MET B4675 " --> pdb=" O ASP B4671 " (cutoff:3.500A) Processing helix chain 'B' and resid 4683 through 4695 removed outlier: 3.540A pdb=" N GLN B4695 " --> pdb=" O LEU B4691 " (cutoff:3.500A) Processing helix chain 'B' and resid 4701 through 4706 removed outlier: 4.139A pdb=" N HIS B4706 " --> pdb=" O ASN B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4737 removed outlier: 4.374A pdb=" N GLN B4737 " --> pdb=" O SER B4734 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4382 through 4386 Processing sheet with id=AA2, first strand: chain 'A' and resid 4414 through 4417 Processing sheet with id=AA3, first strand: chain 'A' and resid 4447 through 4449 Processing sheet with id=AA4, first strand: chain 'A' and resid 4508 through 4512 removed outlier: 3.914A pdb=" N LEU A4490 " --> pdb=" O ILE A4501 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A4471 " --> pdb=" O LEU A4458 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A4570 " --> pdb=" O GLU A4460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 4718 through 4724 removed outlier: 5.618A pdb=" N TYR A4719 " --> pdb=" O PHE A4747 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A4747 " --> pdb=" O TYR A4719 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA A4721 " --> pdb=" O GLY A4745 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY A4745 " --> pdb=" O ALA A4721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 4753 through 4754 Processing sheet with id=AA7, first strand: chain 'A' and resid 4768 through 4769 Processing sheet with id=AA8, first strand: chain 'A' and resid 4781 through 4782 removed outlier: 3.614A pdb=" N CYS A4789 " --> pdb=" O PHE A4782 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 4414 through 4417 Processing sheet with id=AB1, first strand: chain 'B' and resid 4447 through 4449 Processing sheet with id=AB2, first strand: chain 'B' and resid 4508 through 4512 removed outlier: 3.915A pdb=" N LEU B4490 " --> pdb=" O ILE B4501 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B4471 " --> pdb=" O LEU B4458 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B4570 " --> pdb=" O GLU B4460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 4718 through 4724 removed outlier: 5.619A pdb=" N TYR B4719 " --> pdb=" O PHE B4747 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE B4747 " --> pdb=" O TYR B4719 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B4721 " --> pdb=" O GLY B4745 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY B4745 " --> pdb=" O ALA B4721 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4753 through 4754 Processing sheet with id=AB5, first strand: chain 'B' and resid 4768 through 4769 Processing sheet with id=AB6, first strand: chain 'B' and resid 4781 through 4782 removed outlier: 3.615A pdb=" N CYS B4789 " --> pdb=" O PHE B4782 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.77 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1096 1.32 - 1.45: 1818 1.45 - 1.57: 3579 1.57 - 1.70: 1 1.70 - 1.83: 100 Bond restraints: 6594 Sorted by residual: bond pdb=" CA THR A4740 " pdb=" C THR A4740 " ideal model delta sigma weight residual 1.523 1.605 -0.081 1.34e-02 5.57e+03 3.68e+01 bond pdb=" N VAL B4659 " pdb=" CA VAL B4659 " ideal model delta sigma weight residual 1.454 1.495 -0.041 7.70e-03 1.69e+04 2.78e+01 bond pdb=" N VAL A4659 " pdb=" CA VAL A4659 " ideal model delta sigma weight residual 1.454 1.495 -0.040 7.70e-03 1.69e+04 2.73e+01 bond pdb=" N LYS A4609 " pdb=" CA LYS A4609 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.40e-03 1.83e+04 2.23e+01 bond pdb=" N LYS B4609 " pdb=" CA LYS B4609 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.40e-03 1.83e+04 2.16e+01 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 8675 3.34 - 6.69: 301 6.69 - 10.03: 29 10.03 - 13.38: 8 13.38 - 16.72: 9 Bond angle restraints: 9022 Sorted by residual: angle pdb=" N VAL A4741 " pdb=" CA VAL A4741 " pdb=" C VAL A4741 " ideal model delta sigma weight residual 109.51 95.48 14.03 1.43e+00 4.89e-01 9.62e+01 angle pdb=" N ASN A4739 " pdb=" CA ASN A4739 " pdb=" C ASN A4739 " ideal model delta sigma weight residual 113.23 102.85 10.38 1.24e+00 6.50e-01 7.01e+01 angle pdb=" C VAL B4392 " pdb=" N GLU B4393 " pdb=" CA GLU B4393 " ideal model delta sigma weight residual 122.84 112.46 10.38 1.30e+00 5.92e-01 6.37e+01 angle pdb=" C VAL A4392 " pdb=" N GLU A4393 " pdb=" CA GLU A4393 " ideal model delta sigma weight residual 122.84 112.46 10.38 1.30e+00 5.92e-01 6.37e+01 angle pdb=" N GLY B4410 " pdb=" CA GLY B4410 " pdb=" C GLY B4410 " ideal model delta sigma weight residual 114.69 105.23 9.46 1.19e+00 7.06e-01 6.31e+01 ... (remaining 9017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 3365 17.12 - 34.24: 300 34.24 - 51.36: 148 51.36 - 68.48: 66 68.48 - 85.60: 16 Dihedral angle restraints: 3895 sinusoidal: 1529 harmonic: 2366 Sorted by residual: dihedral pdb=" CB CYS B4713 " pdb=" SG CYS B4713 " pdb=" SG CYS B4746 " pdb=" CB CYS B4746 " ideal model delta sinusoidal sigma weight residual -86.00 -162.50 76.50 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A4713 " pdb=" SG CYS A4713 " pdb=" SG CYS A4746 " pdb=" CB CYS A4746 " ideal model delta sinusoidal sigma weight residual -86.00 -162.49 76.49 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS B4682 " pdb=" SG CYS B4682 " pdb=" SG CYS B4709 " pdb=" CB CYS B4709 " ideal model delta sinusoidal sigma weight residual 93.00 164.03 -71.03 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 3892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 950 0.169 - 0.338: 66 0.338 - 0.507: 6 0.507 - 0.676: 2 0.676 - 0.845: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.63e+02 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 -2.02 -0.38 2.00e-02 2.50e+03 3.58e+02 chirality pdb=" C2 BMA C 3 " pdb=" C1 BMA C 3 " pdb=" C3 BMA C 3 " pdb=" O2 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.47 1.63 0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 1023 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.336 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG D 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.335 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG C 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.215 2.00e-02 2.50e+03 1.77e-01 3.92e+02 pdb=" C7 NAG D 2 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.289 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.022 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 168 2.67 - 3.22: 5794 3.22 - 3.78: 9234 3.78 - 4.34: 12507 4.34 - 4.90: 20315 Nonbonded interactions: 48018 Sorted by model distance: nonbonded pdb=" O ASN B4739 " pdb=" CG2 THR B4740 " model vdw 2.107 3.460 nonbonded pdb=" O ASN A4739 " pdb=" CG2 THR A4740 " model vdw 2.191 3.460 nonbonded pdb=" OH TYR B4450 " pdb=" OD1 ASP B4600 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A4450 " pdb=" OD1 ASP A4600 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR B4575 " pdb=" O ASP B4582 " model vdw 2.335 3.040 ... (remaining 48013 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.710 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.008 0.081 6647 Z= 0.597 Angle : 1.484 16.723 9142 Z= 0.961 Chirality : 0.102 0.845 1026 Planarity : 0.016 0.292 1168 Dihedral : 18.068 85.597 2258 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.77 % Favored : 90.98 % Rotamer: Outliers : 14.67 % Allowed : 5.13 % Favored : 80.20 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.29), residues: 798 helix: 0.55 (0.64), residues: 78 sheet: -0.74 (0.39), residues: 190 loop : -1.85 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A4564 TYR 0.018 0.002 TYR B4551 PHE 0.021 0.002 PHE B4652 TRP 0.020 0.002 TRP B4377 HIS 0.003 0.001 HIS A4425 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.60 ( 6594) covalent geometry : angle 1.46524 / 0.96 ( 9022) SS BOND : bond 0.01443 / 1.05 ( 39) SS BOND : angle 2.46217 / 1.62 ( 78) hydrogen bonds : bond 0.17531 / 11.33 ( 186) hydrogen bonds : angle 8.53813 / 5.86 ( 456) link_ALPHA1-3 : bond 0.00172 / 0.12 ( 2) link_ALPHA1-3 : angle 1.16502 / 0.88 ( 6) link_ALPHA1-6 : bond 0.00314 / 0.22 ( 2) link_ALPHA1-6 : angle 1.46958 / 0.99 ( 6) link_BETA1-4 : bond 0.00178 / 0.10 ( 4) link_BETA1-4 : angle 3.13284 / 2.04 ( 12) link_NAG-ASN : bond 0.00383 / 0.23 ( 6) link_NAG-ASN : angle 2.97258 / 2.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 75 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4792 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8461 (pp) REVERT: B 4695 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6030 (mm110) outliers start: 103 outliers final: 31 residues processed: 155 average time/residue: 0.0821 time to fit residues: 16.7290 Evaluate side-chains 85 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4385 THR Chi-restraints excluded: chain A residue 4391 THR Chi-restraints excluded: chain A residue 4406 THR Chi-restraints excluded: chain A residue 4409 ASN Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4473 ILE Chi-restraints excluded: chain A residue 4476 TYR Chi-restraints excluded: chain A residue 4478 CYS Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4654 GLN Chi-restraints excluded: chain A residue 4691 LEU Chi-restraints excluded: chain A residue 4699 LEU Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4782 PHE Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4407 CYS Chi-restraints excluded: chain B residue 4409 ASN Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4486 CYS Chi-restraints excluded: chain B residue 4489 THR Chi-restraints excluded: chain B residue 4548 LEU Chi-restraints excluded: chain B residue 4609 LYS Chi-restraints excluded: chain B residue 4675 MET Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4782 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0020 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4475 ASN A4720 GLN ** B4716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4720 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.107328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081992 restraints weight = 16014.216| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.79 r_work: 0.3258 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6647 Z= 0.156 Angle : 0.751 7.774 9142 Z= 0.374 Chirality : 0.048 0.192 1026 Planarity : 0.005 0.057 1168 Dihedral : 10.182 70.954 920 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.42 % Allowed : 13.53 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.30), residues: 798 helix: 0.51 (0.63), residues: 80 sheet: -0.52 (0.38), residues: 194 loop : -1.57 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B4559 TYR 0.015 0.001 TYR A4476 PHE 0.009 0.001 PHE A4652 TRP 0.008 0.001 TRP A4377 HIS 0.008 0.001 HIS A4716 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 6594) covalent geometry : angle 0.73337 / 0.37 ( 9022) SS BOND : bond 0.00300 / 0.20 ( 39) SS BOND : angle 1.09920 / 0.73 ( 78) hydrogen bonds : bond 0.03327 / 2.09 ( 186) hydrogen bonds : angle 6.25255 / 4.31 ( 456) link_ALPHA1-3 : bond 0.00661 / 0.46 ( 2) link_ALPHA1-3 : angle 1.42846 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00584 / 0.40 ( 2) link_ALPHA1-6 : angle 1.59699 / 0.79 ( 6) link_BETA1-4 : bond 0.00166 / 0.11 ( 4) link_BETA1-4 : angle 1.85126 / 1.29 ( 12) link_NAG-ASN : bond 0.00564 / 0.32 ( 6) link_NAG-ASN : angle 2.74195 / 1.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4609 LYS cc_start: 0.8599 (tttt) cc_final: 0.8316 (tttt) REVERT: A 4675 MET cc_start: 0.9052 (pmm) cc_final: 0.8704 (pmm) REVERT: B 4383 MET cc_start: 0.6853 (tpt) cc_final: 0.6630 (mmm) REVERT: B 4415 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8840 (mtp180) outliers start: 31 outliers final: 17 residues processed: 78 average time/residue: 0.0947 time to fit residues: 9.6939 Evaluate side-chains 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4409 ASN Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4478 CYS Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4654 GLN Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4790 VAL Chi-restraints excluded: chain B residue 4409 ASN Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4477 HIS Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4489 THR Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4782 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.0070 chunk 3 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4716 HIS ** 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 = 0.3845 r_free = 0.3845 target = 0.106023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.080798 restraints weight = 15764.841| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.76 r_work: 0.3241 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6647 Z= 0.120 Angle : 0.641 7.645 9142 Z= 0.322 Chirality : 0.045 0.205 1026 Planarity : 0.004 0.050 1168 Dihedral : 8.019 67.157 884 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.89 % Favored : 93.98 % Rotamer: Outliers : 3.56 % Allowed : 14.67 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.31), residues: 798 helix: 0.74 (0.62), residues: 80 sheet: -0.25 (0.39), residues: 182 loop : -1.18 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4559 TYR 0.039 0.001 TYR A4476 PHE 0.011 0.001 PHE A4782 TRP 0.006 0.001 TRP B4435 HIS 0.006 0.001 HIS B4477 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6594) covalent geometry : angle 0.62993 / 0.32 ( 9022) SS BOND : bond 0.00288 / 0.20 ( 39) SS BOND : angle 0.87420 / 0.56 ( 78) hydrogen bonds : bond 0.02832 / 1.79 ( 186) hydrogen bonds : angle 5.52675 / 3.82 ( 456) link_ALPHA1-3 : bond 0.00367 / 0.25 ( 2) link_ALPHA1-3 : angle 1.62351 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00490 / 0.34 ( 2) link_ALPHA1-6 : angle 1.41073 / 0.84 ( 6) link_BETA1-4 : bond 0.00504 / 0.32 ( 4) link_BETA1-4 : angle 1.27963 / 0.73 ( 12) link_NAG-ASN : bond 0.00196 / 0.13 ( 6) link_NAG-ASN : angle 2.00443 / 0.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4609 LYS cc_start: 0.8593 (tttt) cc_final: 0.8209 (tttt) REVERT: A 4675 MET cc_start: 0.8865 (pmm) cc_final: 0.8435 (pmm) REVERT: A 4688 TYR cc_start: 0.8799 (t80) cc_final: 0.8346 (t80) REVERT: A 4784 PHE cc_start: 0.6004 (t80) cc_final: 0.5619 (t80) REVERT: A 4792 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8500 (pp) REVERT: B 4383 MET cc_start: 0.6897 (tpt) cc_final: 0.6674 (tpt) REVERT: B 4559 ARG cc_start: 0.8990 (tpt-90) cc_final: 0.8783 (ttt90) REVERT: B 4695 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6160 (mm110) REVERT: B 4731 LYS cc_start: 0.8718 (tppt) cc_final: 0.8205 (tppt) outliers start: 25 outliers final: 14 residues processed: 75 average time/residue: 0.0916 time to fit residues: 9.1725 Evaluate side-chains 66 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4654 GLN Chi-restraints excluded: chain A residue 4740 THR Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4409 ASN Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4477 HIS Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4743 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0000 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4720 GLN ** B4716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4720 GLN B4788 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078685 restraints weight = 16029.724| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.75 r_work: 0.3223 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6647 Z= 0.134 Angle : 0.629 7.766 9142 Z= 0.317 Chirality : 0.046 0.213 1026 Planarity : 0.004 0.046 1168 Dihedral : 6.803 60.266 876 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.28 % Allowed : 18.66 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.31), residues: 798 helix: 0.93 (0.62), residues: 80 sheet: -0.15 (0.38), residues: 180 loop : -1.00 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4559 TYR 0.020 0.001 TYR A4476 PHE 0.016 0.002 PHE B4782 TRP 0.017 0.001 TRP B4376 HIS 0.004 0.001 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6594) covalent geometry : angle 0.61993 / 0.31 ( 9022) SS BOND : bond 0.00270 / 0.18 ( 39) SS BOND : angle 0.86365 / 0.53 ( 78) hydrogen bonds : bond 0.02935 / 1.85 ( 186) hydrogen bonds : angle 5.23142 / 3.62 ( 456) link_ALPHA1-3 : bond 0.00497 / 0.34 ( 2) link_ALPHA1-3 : angle 1.56218 / 1.08 ( 6) link_ALPHA1-6 : bond 0.00476 / 0.33 ( 2) link_ALPHA1-6 : angle 1.48730 / 0.89 ( 6) link_BETA1-4 : bond 0.00457 / 0.28 ( 4) link_BETA1-4 : angle 1.41311 / 0.89 ( 12) link_NAG-ASN : bond 0.00258 / 0.15 ( 6) link_NAG-ASN : angle 1.53882 / 0.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8424 (pmm) cc_final: 0.7800 (mmt) REVERT: A 4609 LYS cc_start: 0.8613 (tttt) cc_final: 0.8333 (tttt) REVERT: A 4675 MET cc_start: 0.8788 (pmm) cc_final: 0.8315 (pmm) REVERT: A 4792 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8564 (pp) REVERT: B 4525 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8772 (ttmm) REVERT: B 4695 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6519 (mm110) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.0821 time to fit residues: 6.8619 Evaluate side-chains 52 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4699 LEU Chi-restraints excluded: chain A residue 4744 GLU Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4743 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.099704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073747 restraints weight = 15900.061| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.82 r_work: 0.3094 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6647 Z= 0.160 Angle : 0.651 8.632 9142 Z= 0.328 Chirality : 0.046 0.207 1026 Planarity : 0.004 0.044 1168 Dihedral : 6.280 56.156 871 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.14 % Favored : 92.73 % Rotamer: Outliers : 3.70 % Allowed : 18.52 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.30), residues: 798 helix: 1.09 (0.64), residues: 80 sheet: 0.08 (0.40), residues: 174 loop : -1.08 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B4559 TYR 0.023 0.002 TYR A4688 PHE 0.020 0.002 PHE B4782 TRP 0.007 0.001 TRP A4701 HIS 0.005 0.001 HIS B4477 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6594) covalent geometry : angle 0.63964 / 0.33 ( 9022) SS BOND : bond 0.00319 / 0.22 ( 39) SS BOND : angle 1.08651 / 0.65 ( 78) hydrogen bonds : bond 0.03215 / 2.01 ( 186) hydrogen bonds : angle 5.05124 / 3.54 ( 456) link_ALPHA1-3 : bond 0.00601 / 0.41 ( 2) link_ALPHA1-3 : angle 1.50555 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00462 / 0.32 ( 2) link_ALPHA1-6 : angle 1.50733 / 0.90 ( 6) link_BETA1-4 : bond 0.00571 / 0.35 ( 4) link_BETA1-4 : angle 1.28348 / 0.75 ( 12) link_NAG-ASN : bond 0.00290 / 0.18 ( 6) link_NAG-ASN : angle 1.54310 / 0.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4609 LYS cc_start: 0.8624 (tttt) cc_final: 0.8346 (tttt) REVERT: A 4675 MET cc_start: 0.8686 (pmm) cc_final: 0.8158 (pmm) REVERT: A 4695 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8175 (mm110) REVERT: A 4792 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8544 (pp) REVERT: B 4383 MET cc_start: 0.6976 (tpt) cc_final: 0.6771 (tpt) REVERT: B 4476 TYR cc_start: 0.6029 (m-80) cc_final: 0.5824 (m-80) REVERT: B 4525 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8650 (ttmm) REVERT: B 4646 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 4695 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7115 (mm110) REVERT: B 4783 GLU cc_start: 0.7630 (pt0) cc_final: 0.7032 (tt0) REVERT: B 4792 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8758 (pp) outliers start: 26 outliers final: 12 residues processed: 63 average time/residue: 0.0814 time to fit residues: 7.0268 Evaluate side-chains 58 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4695 GLN Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4646 LEU Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4743 VAL Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A4611 HIS ** 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 = 0.3712 r_free = 0.3712 target = 0.098220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072189 restraints weight = 15761.587| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.81 r_work: 0.3057 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6647 Z= 0.175 Angle : 0.648 7.668 9142 Z= 0.326 Chirality : 0.046 0.211 1026 Planarity : 0.004 0.043 1168 Dihedral : 5.979 55.126 868 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.99 % Allowed : 18.95 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.30), residues: 798 helix: 1.92 (0.67), residues: 68 sheet: 0.20 (0.40), residues: 174 loop : -1.10 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B4559 TYR 0.017 0.002 TYR B4551 PHE 0.014 0.002 PHE B4782 TRP 0.018 0.001 TRP B4376 HIS 0.005 0.001 HIS B4477 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 6594) covalent geometry : angle 0.63952 / 0.32 ( 9022) SS BOND : bond 0.00343 / 0.24 ( 39) SS BOND : angle 0.92818 / 0.56 ( 78) hydrogen bonds : bond 0.03196 / 2.02 ( 186) hydrogen bonds : angle 5.07030 / 3.56 ( 456) link_ALPHA1-3 : bond 0.00529 / 0.37 ( 2) link_ALPHA1-3 : angle 1.44923 / 0.96 ( 6) link_ALPHA1-6 : bond 0.00488 / 0.34 ( 2) link_ALPHA1-6 : angle 1.52983 / 0.92 ( 6) link_BETA1-4 : bond 0.00502 / 0.31 ( 4) link_BETA1-4 : angle 1.33146 / 0.82 ( 12) link_NAG-ASN : bond 0.00247 / 0.15 ( 6) link_NAG-ASN : angle 1.42277 / 0.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4415 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8254 (mtp180) REVERT: A 4507 MET cc_start: 0.8589 (pmm) cc_final: 0.8095 (mmt) REVERT: A 4609 LYS cc_start: 0.8570 (tttt) cc_final: 0.8323 (tttt) REVERT: A 4675 MET cc_start: 0.8624 (pmm) cc_final: 0.8055 (pmm) REVERT: A 4695 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8178 (mm110) REVERT: A 4792 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8579 (pp) REVERT: B 4476 TYR cc_start: 0.6086 (m-80) cc_final: 0.5769 (m-80) REVERT: B 4525 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8612 (ttmm) REVERT: B 4695 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7511 (mm-40) REVERT: B 4743 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8998 (m) REVERT: B 4783 GLU cc_start: 0.8090 (pt0) cc_final: 0.7644 (tt0) REVERT: B 4792 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8758 (pp) outliers start: 28 outliers final: 10 residues processed: 64 average time/residue: 0.0768 time to fit residues: 6.5521 Evaluate side-chains 56 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4695 GLN Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4743 VAL Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A4611 HIS ** 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 = 0.3727 r_free = 0.3727 target = 0.099206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073315 restraints weight = 15831.167| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.79 r_work: 0.3086 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6647 Z= 0.120 Angle : 0.614 6.137 9142 Z= 0.307 Chirality : 0.044 0.156 1026 Planarity : 0.004 0.043 1168 Dihedral : 5.655 55.588 866 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.42 % Allowed : 19.37 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.30), residues: 798 helix: 2.02 (0.66), residues: 68 sheet: 0.24 (0.41), residues: 174 loop : -1.11 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B4559 TYR 0.015 0.001 TYR A4476 PHE 0.014 0.001 PHE B4782 TRP 0.007 0.001 TRP A4426 HIS 0.002 0.000 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6594) covalent geometry : angle 0.60611 / 0.31 ( 9022) SS BOND : bond 0.00236 / 0.16 ( 39) SS BOND : angle 0.74490 / 0.46 ( 78) hydrogen bonds : bond 0.02750 / 1.72 ( 186) hydrogen bonds : angle 4.88558 / 3.41 ( 456) link_ALPHA1-3 : bond 0.00555 / 0.38 ( 2) link_ALPHA1-3 : angle 1.47320 / 0.97 ( 6) link_ALPHA1-6 : bond 0.00515 / 0.35 ( 2) link_ALPHA1-6 : angle 1.50585 / 0.88 ( 6) link_BETA1-4 : bond 0.00554 / 0.34 ( 4) link_BETA1-4 : angle 1.23228 / 0.74 ( 12) link_NAG-ASN : bond 0.00223 / 0.14 ( 6) link_NAG-ASN : angle 1.52835 / 0.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8595 (pmm) cc_final: 0.7967 (mmt) REVERT: A 4609 LYS cc_start: 0.8607 (tttt) cc_final: 0.8360 (tttt) REVERT: A 4675 MET cc_start: 0.8552 (pmm) cc_final: 0.8023 (pmm) REVERT: A 4695 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8171 (mm110) REVERT: A 4792 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8524 (pp) REVERT: B 4376 TRP cc_start: 0.5696 (t60) cc_final: 0.5417 (t60) REVERT: B 4415 ARG cc_start: 0.8869 (mtp180) cc_final: 0.8063 (mtp85) REVERT: B 4476 TYR cc_start: 0.6057 (m-80) cc_final: 0.5730 (m-80) REVERT: B 4525 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8522 (ttmm) REVERT: B 4695 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7507 (mm110) REVERT: B 4783 GLU cc_start: 0.7843 (pt0) cc_final: 0.7379 (tt0) REVERT: B 4792 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8752 (pp) outliers start: 24 outliers final: 12 residues processed: 62 average time/residue: 0.0928 time to fit residues: 7.5053 Evaluate side-chains 58 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4695 GLN Chi-restraints excluded: chain A residue 4740 THR Chi-restraints excluded: chain A residue 4764 LYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.0040 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 overall best weight: 0.2510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4611 HIS ** B4716 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 = 0.3747 r_free = 0.3747 target = 0.100419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074676 restraints weight = 15612.359| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.75 r_work: 0.3115 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6647 Z= 0.103 Angle : 0.587 6.709 9142 Z= 0.293 Chirality : 0.043 0.134 1026 Planarity : 0.004 0.042 1168 Dihedral : 5.342 55.284 866 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.36 % Rotamer: Outliers : 2.85 % Allowed : 19.66 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.30), residues: 798 helix: 0.95 (0.62), residues: 80 sheet: 0.36 (0.41), residues: 172 loop : -1.05 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B4559 TYR 0.012 0.001 TYR A4476 PHE 0.011 0.001 PHE B4782 TRP 0.008 0.001 TRP B4376 HIS 0.002 0.000 HIS B4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 6594) covalent geometry : angle 0.58095 / 0.29 ( 9022) SS BOND : bond 0.00212 / 0.14 ( 39) SS BOND : angle 0.60124 / 0.38 ( 78) hydrogen bonds : bond 0.02491 / 1.56 ( 186) hydrogen bonds : angle 4.72463 / 3.31 ( 456) link_ALPHA1-3 : bond 0.00523 / 0.36 ( 2) link_ALPHA1-3 : angle 1.46339 / 0.97 ( 6) link_ALPHA1-6 : bond 0.00523 / 0.36 ( 2) link_ALPHA1-6 : angle 1.48652 / 0.88 ( 6) link_BETA1-4 : bond 0.00537 / 0.32 ( 4) link_BETA1-4 : angle 1.20151 / 0.74 ( 12) link_NAG-ASN : bond 0.00214 / 0.13 ( 6) link_NAG-ASN : angle 1.42429 / 0.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8624 (pmm) cc_final: 0.8121 (mmt) REVERT: A 4675 MET cc_start: 0.8470 (pmm) cc_final: 0.7907 (pmm) REVERT: A 4792 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8513 (pp) REVERT: B 4376 TRP cc_start: 0.5704 (t60) cc_final: 0.5215 (t-100) REVERT: B 4415 ARG cc_start: 0.8860 (mtp180) cc_final: 0.8080 (mtp85) REVERT: B 4476 TYR cc_start: 0.6118 (m-80) cc_final: 0.5862 (m-80) REVERT: B 4525 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8489 (ttmm) REVERT: B 4695 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7456 (mm110) REVERT: B 4783 GLU cc_start: 0.7923 (pt0) cc_final: 0.7524 (tt0) REVERT: B 4792 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8745 (pp) outliers start: 20 outliers final: 10 residues processed: 58 average time/residue: 0.0929 time to fit residues: 7.2102 Evaluate side-chains 51 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4740 THR Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4716 HIS ** 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 = 0.3733 r_free = 0.3733 target = 0.099570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073590 restraints weight = 15995.029| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.81 r_work: 0.3088 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6647 Z= 0.121 Angle : 0.599 6.513 9142 Z= 0.300 Chirality : 0.044 0.139 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.364 54.952 866 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.36 % Rotamer: Outliers : 2.14 % Allowed : 21.23 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.30), residues: 798 helix: 2.02 (0.65), residues: 68 sheet: 0.33 (0.41), residues: 174 loop : -1.10 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4559 TYR 0.011 0.001 TYR A4476 PHE 0.012 0.001 PHE B4782 TRP 0.005 0.001 TRP A4426 HIS 0.004 0.001 HIS A4477 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6594) covalent geometry : angle 0.59177 / 0.30 ( 9022) SS BOND : bond 0.00215 / 0.15 ( 39) SS BOND : angle 0.72803 / 0.45 ( 78) hydrogen bonds : bond 0.02761 / 1.73 ( 186) hydrogen bonds : angle 4.72867 / 3.31 ( 456) link_ALPHA1-3 : bond 0.00558 / 0.38 ( 2) link_ALPHA1-3 : angle 1.47017 / 0.97 ( 6) link_ALPHA1-6 : bond 0.00508 / 0.35 ( 2) link_ALPHA1-6 : angle 1.50151 / 0.89 ( 6) link_BETA1-4 : bond 0.00532 / 0.32 ( 4) link_BETA1-4 : angle 1.20408 / 0.73 ( 12) link_NAG-ASN : bond 0.00201 / 0.12 ( 6) link_NAG-ASN : angle 1.37411 / 0.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8676 (pmm) cc_final: 0.8137 (mmt) REVERT: A 4509 MET cc_start: 0.8156 (ptm) cc_final: 0.7897 (ptp) REVERT: A 4609 LYS cc_start: 0.8873 (tttt) cc_final: 0.8137 (ttpt) REVERT: A 4675 MET cc_start: 0.8471 (pmm) cc_final: 0.7921 (pmm) REVERT: A 4792 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8544 (pp) REVERT: B 4376 TRP cc_start: 0.5715 (t60) cc_final: 0.5176 (t-100) REVERT: B 4476 TYR cc_start: 0.6172 (m-80) cc_final: 0.5802 (m-80) REVERT: B 4525 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8504 (ttmm) REVERT: B 4695 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7583 (mm110) REVERT: B 4783 GLU cc_start: 0.7934 (pt0) cc_final: 0.7584 (tt0) REVERT: B 4792 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8738 (pp) outliers start: 15 outliers final: 9 residues processed: 52 average time/residue: 0.0910 time to fit residues: 6.4017 Evaluate side-chains 52 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4740 THR Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4716 HIS ** 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 = 0.3705 r_free = 0.3705 target = 0.097907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071949 restraints weight = 15640.429| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.76 r_work: 0.3056 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6647 Z= 0.164 Angle : 0.636 7.209 9142 Z= 0.319 Chirality : 0.045 0.147 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.522 55.775 866 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 2.42 % Allowed : 20.94 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.30), residues: 798 helix: 1.64 (0.66), residues: 72 sheet: 0.38 (0.40), residues: 174 loop : -1.14 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A4559 TYR 0.014 0.001 TYR A4551 PHE 0.014 0.001 PHE B4782 TRP 0.005 0.001 TRP B4424 HIS 0.003 0.001 HIS A4716 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 6594) covalent geometry : angle 0.62796 / 0.32 ( 9022) SS BOND : bond 0.00286 / 0.20 ( 39) SS BOND : angle 0.90666 / 0.56 ( 78) hydrogen bonds : bond 0.03121 / 1.96 ( 186) hydrogen bonds : angle 4.83057 / 3.40 ( 456) link_ALPHA1-3 : bond 0.00562 / 0.39 ( 2) link_ALPHA1-3 : angle 1.43729 / 0.94 ( 6) link_ALPHA1-6 : bond 0.00516 / 0.35 ( 2) link_ALPHA1-6 : angle 1.53294 / 0.92 ( 6) link_BETA1-4 : bond 0.00537 / 0.33 ( 4) link_BETA1-4 : angle 1.25345 / 0.77 ( 12) link_NAG-ASN : bond 0.00240 / 0.15 ( 6) link_NAG-ASN : angle 1.38131 / 0.63 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8661 (pmm) cc_final: 0.8211 (mmt) REVERT: A 4509 MET cc_start: 0.8331 (ptm) cc_final: 0.8095 (ptp) REVERT: A 4609 LYS cc_start: 0.8844 (tttt) cc_final: 0.8617 (tttt) REVERT: A 4675 MET cc_start: 0.8507 (pmm) cc_final: 0.7910 (pmm) REVERT: A 4695 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8211 (mm110) REVERT: A 4792 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8522 (pp) REVERT: B 4476 TYR cc_start: 0.6158 (m-80) cc_final: 0.5787 (m-80) REVERT: B 4525 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8563 (ttmm) REVERT: B 4695 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7750 (mm110) REVERT: B 4783 GLU cc_start: 0.8060 (pt0) cc_final: 0.7652 (tt0) REVERT: B 4792 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8743 (pp) outliers start: 17 outliers final: 10 residues processed: 51 average time/residue: 0.0895 time to fit residues: 6.2848 Evaluate side-chains 54 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4522 LEU Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4592 VAL Chi-restraints excluded: chain A residue 4695 GLN Chi-restraints excluded: chain A residue 4740 THR Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4525 LYS Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4695 GLN Chi-restraints excluded: chain B residue 4792 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4716 HIS ** 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 = 0.3723 r_free = 0.3723 target = 0.099011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.073119 restraints weight = 15703.387| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.77 r_work: 0.3081 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6647 Z= 0.116 Angle : 0.599 7.514 9142 Z= 0.298 Chirality : 0.044 0.137 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.431 57.233 866 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.64 % Favored : 93.23 % Rotamer: Outliers : 1.99 % Allowed : 21.65 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.30), residues: 798 helix: 2.01 (0.66), residues: 68 sheet: 0.37 (0.40), residues: 174 loop : -1.10 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4559 TYR 0.012 0.001 TYR A4476 PHE 0.012 0.001 PHE B4782 TRP 0.015 0.001 TRP B4376 HIS 0.002 0.001 HIS A4611 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6594) covalent geometry : angle 0.59244 / 0.30 ( 9022) SS BOND : bond 0.00218 / 0.15 ( 39) SS BOND : angle 0.69128 / 0.43 ( 78) hydrogen bonds : bond 0.02646 / 1.66 ( 186) hydrogen bonds : angle 4.69974 / 3.31 ( 456) link_ALPHA1-3 : bond 0.00551 / 0.38 ( 2) link_ALPHA1-3 : angle 1.43902 / 0.95 ( 6) link_ALPHA1-6 : bond 0.00541 / 0.37 ( 2) link_ALPHA1-6 : angle 1.51553 / 0.89 ( 6) link_BETA1-4 : bond 0.00537 / 0.32 ( 4) link_BETA1-4 : angle 1.18542 / 0.72 ( 12) link_NAG-ASN : bond 0.00219 / 0.13 ( 6) link_NAG-ASN : angle 1.38962 / 0.63 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.16 seconds wall clock time: 28 minutes 41.88 seconds (1721.88 seconds total)