Starting phenix.real_space_refine on Tue Feb 11 22:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qcn_13897/02_2025/7qcn_13897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qcn_13897/02_2025/7qcn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qcn_13897/02_2025/7qcn_13897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qcn_13897/02_2025/7qcn_13897.map" model { file = "/net/cci-nas-00/data/ceres_data/7qcn_13897/02_2025/7qcn_13897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qcn_13897/02_2025/7qcn_13897.cif" } resolution = 3.4 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3} 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: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3} 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 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: 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.82, per 1000 atoms: 0.75 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: 1.84 Conformation dependent library (CDL) restraints added in 932.6 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: 0.73 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: 1.79 Time building geometry restraints manager: 2.12 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 - 18.76: 3701 18.76 - 37.52: 309 37.52 - 56.28: 139 56.28 - 75.04: 52 75.04 - 93.80: 18 Dihedral angle restraints: 4219 sinusoidal: 1853 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 4216 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: 0.03 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: 5.530 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.720 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 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 6594 Z= 0.556 Angle : 1.465 16.723 9022 Z= 0.959 Chirality : 0.102 0.845 1026 Planarity : 0.016 0.292 1168 Dihedral : 18.424 93.801 2582 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 (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: -1.90 (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 TRP 0.020 0.002 TRP B4377 HIS 0.003 0.001 HIS A4425 PHE 0.021 0.002 PHE B4652 TYR 0.018 0.002 TYR B4551 ARG 0.011 0.001 ARG A4564 *********************** 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 : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4688 TYR cc_start: 0.8198 (t80) cc_final: 0.7825 (t80) REVERT: A 4792 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8462 (pp) REVERT: B 4695 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6030 (mm110) outliers start: 103 outliers final: 31 residues processed: 155 average time/residue: 0.1959 time to fit residues: 39.3123 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 : 0.683 ------------------------------------------------------------------------------- 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 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 38 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3855 r_free = 0.3855 target = 0.106646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081273 restraints weight = 15708.629| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.75 r_work: 0.3246 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6594 Z= 0.254 Angle : 0.750 7.565 9022 Z= 0.378 Chirality : 0.049 0.201 1026 Planarity : 0.005 0.057 1168 Dihedral : 11.634 70.779 1244 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.56 % Allowed : 13.53 % Favored : 81.91 % 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: -1.56 (0.30), residues: 798 helix: 0.61 (0.63), residues: 80 sheet: -0.50 (0.38), residues: 194 loop : -1.59 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A4377 HIS 0.007 0.001 HIS A4716 PHE 0.011 0.001 PHE A4652 TYR 0.014 0.001 TYR A4688 ARG 0.003 0.000 ARG B4559 *********************** 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 83 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4609 LYS cc_start: 0.8604 (tttt) cc_final: 0.8285 (tttt) REVERT: A 4675 MET cc_start: 0.9084 (pmm) cc_final: 0.8776 (pmm) REVERT: B 4383 MET cc_start: 0.6841 (tpt) cc_final: 0.6613 (mmm) REVERT: B 4415 ARG cc_start: 0.9107 (mtp180) cc_final: 0.8704 (mtp180) REVERT: B 4476 TYR cc_start: 0.6001 (m-80) cc_final: 0.5787 (m-80) outliers start: 32 outliers final: 16 residues processed: 78 average time/residue: 0.2159 time to fit residues: 21.9198 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 : 0.836 ------------------------------------------------------------------------------- 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 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 4764 LYS 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 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.0040 chunk 68 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4720 GLN ** 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 = 0.3802 r_free = 0.3802 target = 0.103480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077443 restraints weight = 15862.330| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.82 r_work: 0.3162 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6594 Z= 0.215 Angle : 0.658 7.755 9022 Z= 0.331 Chirality : 0.047 0.200 1026 Planarity : 0.005 0.049 1168 Dihedral : 8.584 63.961 1206 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.28 % Allowed : 16.67 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.11 (0.31), residues: 798 helix: 0.81 (0.63), residues: 80 sheet: -0.25 (0.39), residues: 182 loop : -1.21 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A4435 HIS 0.005 0.001 HIS B4611 PHE 0.013 0.001 PHE A4782 TYR 0.035 0.002 TYR A4476 ARG 0.003 0.000 ARG A4559 *********************** 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 78 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4609 LYS cc_start: 0.8525 (tttt) cc_final: 0.8258 (tttt) REVERT: A 4675 MET cc_start: 0.8833 (pmm) cc_final: 0.8389 (pmm) REVERT: A 4688 TYR cc_start: 0.9026 (t80) cc_final: 0.8731 (t80) REVERT: A 4792 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8524 (pp) REVERT: B 4383 MET cc_start: 0.6964 (tpt) cc_final: 0.6721 (tpt) REVERT: B 4415 ARG cc_start: 0.9027 (mtp180) cc_final: 0.8742 (mtp180) REVERT: B 4476 TYR cc_start: 0.6167 (m-80) cc_final: 0.5919 (m-80) REVERT: B 4559 ARG cc_start: 0.9030 (tpt-90) cc_final: 0.8764 (ttm-80) REVERT: B 4695 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6559 (mm110) outliers start: 23 outliers final: 12 residues processed: 73 average time/residue: 0.2125 time to fit residues: 20.5213 Evaluate side-chains 61 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 76 optimal weight: 0.0670 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4720 GLN B4788 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.103150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077661 restraints weight = 15954.937| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.78 r_work: 0.3174 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6594 Z= 0.165 Angle : 0.597 7.688 9022 Z= 0.299 Chirality : 0.045 0.203 1026 Planarity : 0.004 0.047 1168 Dihedral : 7.229 60.258 1200 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 2.42 % Allowed : 18.80 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.31), residues: 798 helix: 0.82 (0.62), residues: 80 sheet: -0.24 (0.38), residues: 182 loop : -1.03 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B4376 HIS 0.005 0.001 HIS B4611 PHE 0.010 0.001 PHE B4782 TYR 0.016 0.001 TYR A4476 ARG 0.001 0.000 ARG A4559 *********************** 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 62 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8503 (pmm) cc_final: 0.7761 (mmt) REVERT: A 4609 LYS cc_start: 0.8554 (tttt) cc_final: 0.8319 (tttt) REVERT: A 4675 MET cc_start: 0.8718 (pmm) cc_final: 0.8197 (pmm) REVERT: A 4792 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8497 (pp) REVERT: B 4376 TRP cc_start: 0.5715 (t60) cc_final: 0.5348 (t-100) REVERT: B 4383 MET cc_start: 0.6929 (tpt) cc_final: 0.6720 (tpt) REVERT: B 4476 TYR cc_start: 0.6067 (m-80) cc_final: 0.5693 (m-80) REVERT: B 4525 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8730 (ttmm) REVERT: B 4695 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6495 (mm110) REVERT: B 4783 GLU cc_start: 0.6933 (pt0) cc_final: 0.6290 (tt0) outliers start: 17 outliers final: 10 residues processed: 59 average time/residue: 0.1949 time to fit residues: 15.4388 Evaluate side-chains 55 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.100283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.074449 restraints weight = 15737.503| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.79 r_work: 0.3108 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6594 Z= 0.226 Angle : 0.622 7.580 9022 Z= 0.316 Chirality : 0.046 0.213 1026 Planarity : 0.004 0.043 1168 Dihedral : 6.464 56.148 1195 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.14 % Favored : 92.73 % Rotamer: Outliers : 3.28 % Allowed : 18.52 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.88 (0.30), residues: 798 helix: 0.94 (0.63), residues: 80 sheet: 0.03 (0.39), residues: 174 loop : -1.08 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B4376 HIS 0.004 0.001 HIS B4611 PHE 0.013 0.001 PHE A4782 TYR 0.018 0.001 TYR B4551 ARG 0.006 0.000 ARG B4559 *********************** 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 69 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8538 (pmm) cc_final: 0.7802 (mmt) REVERT: A 4609 LYS cc_start: 0.8584 (tttt) cc_final: 0.8272 (tttt) REVERT: A 4675 MET cc_start: 0.8686 (pmm) cc_final: 0.8151 (pmm) REVERT: A 4695 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8215 (mm110) REVERT: A 4791 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7698 (t) REVERT: A 4792 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8529 (pp) REVERT: B 4376 TRP cc_start: 0.5778 (t60) cc_final: 0.5329 (t-100) REVERT: B 4415 ARG cc_start: 0.8976 (mtp180) cc_final: 0.8136 (mtp85) REVERT: B 4476 TYR cc_start: 0.6313 (m-80) cc_final: 0.6058 (m-80) REVERT: B 4525 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8670 (ttmm) REVERT: B 4646 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 4695 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7051 (mm110) REVERT: B 4783 GLU cc_start: 0.7775 (pt0) cc_final: 0.7242 (tt0) REVERT: B 4792 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8759 (pp) outliers start: 23 outliers final: 11 residues processed: 65 average time/residue: 0.2294 time to fit residues: 19.3881 Evaluate side-chains 56 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 4791 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 4646 LEU Chi-restraints excluded: chain B residue 4695 GLN 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 45 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 0.0010 chunk 20 optimal weight: 0.0570 chunk 61 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 71 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3761 r_free = 0.3761 target = 0.101166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075494 restraints weight = 15636.449| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.76 r_work: 0.3129 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6594 Z= 0.172 Angle : 0.594 7.687 9022 Z= 0.298 Chirality : 0.045 0.209 1026 Planarity : 0.004 0.044 1168 Dihedral : 5.963 56.494 1192 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 3.42 % Allowed : 18.38 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.30), residues: 798 helix: 1.91 (0.65), residues: 68 sheet: 0.14 (0.40), residues: 174 loop : -1.04 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B4426 HIS 0.004 0.001 HIS B4611 PHE 0.012 0.001 PHE A4782 TYR 0.013 0.001 TYR A4476 ARG 0.006 0.000 ARG A4559 *********************** 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 66 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8504 (pmm) cc_final: 0.7879 (mmt) REVERT: A 4609 LYS cc_start: 0.8624 (tttt) cc_final: 0.8389 (tttt) REVERT: A 4675 MET cc_start: 0.8591 (pmm) cc_final: 0.8093 (pmm) REVERT: A 4792 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 4376 TRP cc_start: 0.5806 (t60) cc_final: 0.5326 (t-100) REVERT: B 4383 MET cc_start: 0.7114 (tpt) cc_final: 0.6884 (tpt) REVERT: B 4415 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8097 (mtp85) REVERT: B 4476 TYR cc_start: 0.6358 (m-80) cc_final: 0.5948 (m-80) REVERT: B 4525 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8594 (ttmm) REVERT: B 4609 LYS cc_start: 0.7069 (tttt) cc_final: 0.6671 (ttmt) REVERT: B 4695 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7001 (mm110) REVERT: B 4783 GLU cc_start: 0.7452 (pt0) cc_final: 0.6913 (tt0) REVERT: B 4792 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8768 (pp) outliers start: 24 outliers final: 10 residues processed: 62 average time/residue: 0.1798 time to fit residues: 15.4202 Evaluate side-chains 54 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 4611 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 70 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.099905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074063 restraints weight = 15631.802| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.76 r_work: 0.3103 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6594 Z= 0.208 Angle : 0.604 6.363 9022 Z= 0.303 Chirality : 0.045 0.186 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.748 55.929 1190 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.70 % Allowed : 18.80 % 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 (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: -0.72 (0.30), residues: 798 helix: 1.98 (0.66), residues: 68 sheet: 0.09 (0.40), residues: 186 loop : -1.07 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B4376 HIS 0.003 0.001 HIS B4611 PHE 0.020 0.001 PHE A4784 TYR 0.013 0.001 TYR A4476 ARG 0.004 0.000 ARG A4559 *********************** 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 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8556 (pmm) cc_final: 0.7966 (mmt) REVERT: A 4609 LYS cc_start: 0.8596 (tttt) cc_final: 0.8282 (tttt) REVERT: A 4675 MET cc_start: 0.8558 (pmm) cc_final: 0.8060 (pmm) REVERT: A 4695 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (mm110) REVERT: A 4753 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8417 (ppp) REVERT: A 4792 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8561 (pp) REVERT: B 4376 TRP cc_start: 0.5869 (t60) cc_final: 0.5309 (t-100) REVERT: B 4383 MET cc_start: 0.7085 (tpt) cc_final: 0.6867 (tpt) REVERT: B 4476 TYR cc_start: 0.6655 (m-80) cc_final: 0.6260 (m-80) REVERT: B 4525 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8596 (ttmm) REVERT: B 4695 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7186 (mm110) REVERT: B 4783 GLU cc_start: 0.7889 (pt0) cc_final: 0.7449 (tt0) REVERT: B 4792 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8752 (pp) outliers start: 26 outliers final: 12 residues processed: 58 average time/residue: 0.1892 time to fit residues: 15.2168 Evaluate side-chains 55 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 4509 MET Chi-restraints excluded: chain A residue 4548 LEU 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 4753 MET Chi-restraints excluded: chain A residue 4786 CYS Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain B residue 4453 ASN 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 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073811 restraints weight = 15472.677| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.75 r_work: 0.3096 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 0.046 6594 Z= 0.206 Angle : 0.603 6.225 9022 Z= 0.303 Chirality : 0.045 0.142 1026 Planarity : 0.004 0.040 1168 Dihedral : 5.582 56.510 1190 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.71 % Allowed : 19.66 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.30), residues: 798 helix: 1.94 (0.65), residues: 68 sheet: 0.27 (0.41), residues: 174 loop : -1.09 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B4376 HIS 0.004 0.001 HIS B4611 PHE 0.020 0.001 PHE A4784 TYR 0.013 0.001 TYR A4476 ARG 0.005 0.000 ARG A4559 *********************** 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 61 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8605 (pmm) cc_final: 0.8064 (mmt) REVERT: A 4609 LYS cc_start: 0.8620 (tttt) cc_final: 0.8312 (tttt) REVERT: A 4675 MET cc_start: 0.8519 (pmm) cc_final: 0.7923 (pmm) REVERT: A 4695 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8166 (mm110) REVERT: A 4753 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8373 (ppp) REVERT: A 4792 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8514 (pp) REVERT: B 4383 MET cc_start: 0.7085 (tpt) cc_final: 0.6872 (tpt) REVERT: B 4476 TYR cc_start: 0.6449 (m-80) cc_final: 0.6109 (m-80) REVERT: B 4525 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8529 (ttmm) REVERT: B 4695 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7416 (mm110) REVERT: B 4783 GLU cc_start: 0.7844 (pt0) cc_final: 0.7442 (tt0) REVERT: B 4792 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8747 (pp) outliers start: 19 outliers final: 9 residues processed: 56 average time/residue: 0.2017 time to fit residues: 15.1513 Evaluate side-chains 53 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 4611 HIS Chi-restraints excluded: chain A residue 4695 GLN Chi-restraints excluded: chain A residue 4753 MET 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 74 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 6 optimal weight: 0.3980 chunk 63 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3744 r_free = 0.3744 target = 0.100171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074202 restraints weight = 15764.879| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.80 r_work: 0.3102 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6594 Z= 0.179 Angle : 0.590 6.565 9022 Z= 0.296 Chirality : 0.044 0.140 1026 Planarity : 0.004 0.040 1168 Dihedral : 5.415 57.119 1190 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 2.56 % Allowed : 20.09 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.30), residues: 798 helix: 1.96 (0.65), residues: 68 sheet: 0.37 (0.41), residues: 172 loop : -1.12 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B4376 HIS 0.002 0.000 HIS A4716 PHE 0.021 0.001 PHE A4784 TYR 0.012 0.001 TYR A4476 ARG 0.004 0.000 ARG A4559 *********************** 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 59 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4415 ARG cc_start: 0.8763 (mtp180) cc_final: 0.8498 (mtp85) REVERT: A 4507 MET cc_start: 0.8642 (pmm) cc_final: 0.8069 (mmt) REVERT: A 4509 MET cc_start: 0.7988 (tmm) cc_final: 0.7716 (ptp) REVERT: A 4609 LYS cc_start: 0.8617 (tttt) cc_final: 0.8394 (tttt) REVERT: A 4675 MET cc_start: 0.8507 (pmm) cc_final: 0.7913 (pmm) REVERT: A 4695 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8132 (mm110) REVERT: A 4753 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8367 (ppp) REVERT: A 4792 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8539 (pp) REVERT: B 4476 TYR cc_start: 0.6599 (m-80) cc_final: 0.6073 (m-80) REVERT: B 4525 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8512 (ttmm) REVERT: B 4609 LYS cc_start: 0.7351 (tttt) cc_final: 0.6966 (ttmt) REVERT: B 4695 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7422 (mm110) REVERT: B 4783 GLU cc_start: 0.7928 (pt0) cc_final: 0.7605 (tt0) REVERT: B 4792 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8732 (pp) outliers start: 18 outliers final: 8 residues processed: 55 average time/residue: 0.2303 time to fit residues: 16.8050 Evaluate side-chains 54 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 4753 MET 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 6 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3706 r_free = 0.3706 target = 0.097911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071993 restraints weight = 15614.149| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.78 r_work: 0.3056 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6594 Z= 0.265 Angle : 0.634 6.944 9022 Z= 0.319 Chirality : 0.046 0.151 1026 Planarity : 0.004 0.039 1168 Dihedral : 5.607 57.346 1190 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.56 % Allowed : 20.09 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.30), residues: 798 helix: 1.98 (0.67), residues: 68 sheet: 0.34 (0.40), residues: 174 loop : -1.18 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B4376 HIS 0.004 0.001 HIS A4716 PHE 0.021 0.002 PHE A4784 TYR 0.014 0.001 TYR A4476 ARG 0.004 0.001 ARG A4559 ********************** 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 59 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4415 ARG cc_start: 0.8881 (mtp180) cc_final: 0.8537 (mtp85) REVERT: A 4507 MET cc_start: 0.8666 (pmm) cc_final: 0.8157 (mmt) REVERT: A 4509 MET cc_start: 0.8145 (tmm) cc_final: 0.7912 (ptp) REVERT: A 4609 LYS cc_start: 0.8590 (tttt) cc_final: 0.8389 (tttt) REVERT: A 4675 MET cc_start: 0.8542 (pmm) cc_final: 0.7961 (pmm) REVERT: A 4695 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8216 (mm110) REVERT: A 4753 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8401 (ppp) REVERT: A 4792 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8545 (pp) REVERT: B 4476 TYR cc_start: 0.6653 (m-80) cc_final: 0.6169 (m-80) REVERT: B 4525 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8575 (ttmm) REVERT: B 4609 LYS cc_start: 0.7445 (tttt) cc_final: 0.7035 (ttmt) REVERT: B 4695 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7681 (mm110) REVERT: B 4783 GLU cc_start: 0.8069 (pt0) cc_final: 0.7712 (tt0) REVERT: B 4792 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8724 (pp) outliers start: 18 outliers final: 10 residues processed: 53 average time/residue: 0.2182 time to fit residues: 15.3865 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 : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4383 MET Chi-restraints excluded: chain A residue 4428 CYS Chi-restraints excluded: chain A residue 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 4753 MET 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 75 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 54 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3737 r_free = 0.3737 target = 0.099802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073934 restraints weight = 15846.386| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.81 r_work: 0.3102 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6594 Z= 0.165 Angle : 0.590 7.515 9022 Z= 0.296 Chirality : 0.044 0.137 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.347 59.174 1190 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 2.28 % Allowed : 20.51 % 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 (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: -0.66 (0.30), residues: 798 helix: 1.99 (0.65), residues: 68 sheet: 0.46 (0.41), residues: 172 loop : -1.12 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4424 HIS 0.002 0.001 HIS B4563 PHE 0.020 0.001 PHE A4784 TYR 0.011 0.001 TYR A4476 ARG 0.004 0.000 ARG A4559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.92 seconds wall clock time: 57 minutes 52.44 seconds (3472.44 seconds total)