Starting phenix.real_space_refine on Tue Mar 11 21:55:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qcn_13897/03_2025/7qcn_13897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qcn_13897/03_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_13897/03_2025/7qcn_13897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qcn_13897/03_2025/7qcn_13897.map" model { file = "/net/cci-nas-00/data/ceres_data/7qcn_13897/03_2025/7qcn_13897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qcn_13897/03_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-5624/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: 5.24, per 1000 atoms: 0.82 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: 1.81 Conformation dependent library (CDL) restraints added in 915.9 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: 0.76 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: 1.63 Time building geometry restraints manager: 2.13 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: 5.710 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.500 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- 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 : 0.722 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: 0.2149 time to fit residues: 43.2466 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 : 0.697 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081278 restraints weight = 15708.639| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.75 r_work: 0.3247 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- 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 : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4609 LYS cc_start: 0.8604 (tttt) cc_final: 0.8287 (tttt) REVERT: A 4675 MET cc_start: 0.9085 (pmm) cc_final: 0.8777 (pmm) REVERT: B 4383 MET cc_start: 0.6840 (tpt) cc_final: 0.6613 (mmm) REVERT: B 4415 ARG cc_start: 0.9110 (mtp180) cc_final: 0.8706 (mtp180) REVERT: B 4476 TYR cc_start: 0.5998 (m-80) cc_final: 0.5783 (m-80) outliers start: 32 outliers final: 16 residues processed: 78 average time/residue: 0.2182 time to fit residues: 22.1726 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 : 0.707 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4720 GLN ** B4716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4720 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.102118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075889 restraints weight = 15845.572| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.83 r_work: 0.3141 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6594 Z= 0.261 Angle : 0.682 7.466 9022 Z= 0.346 Chirality : 0.048 0.228 1026 Planarity : 0.005 0.049 1168 Dihedral : 8.879 62.811 1206 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.56 % Allowed : 15.81 % Favored : 80.63 % 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: -1.16 (0.31), residues: 798 helix: 0.80 (0.64), residues: 80 sheet: -0.26 (0.38), residues: 182 loop : -1.26 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A4435 HIS 0.009 0.001 HIS B4477 PHE 0.013 0.002 PHE A4565 TYR 0.043 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 79 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4609 LYS cc_start: 0.8558 (tttt) cc_final: 0.8185 (tttt) REVERT: A 4675 MET cc_start: 0.8895 (pmm) cc_final: 0.8496 (pmm) REVERT: A 4791 CYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7629 (t) REVERT: A 4792 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8553 (pp) REVERT: B 4383 MET cc_start: 0.7018 (tpt) cc_final: 0.6773 (tpt) REVERT: B 4476 TYR cc_start: 0.6152 (m-80) cc_final: 0.5857 (m-80) REVERT: B 4559 ARG cc_start: 0.9079 (tpt-90) cc_final: 0.8817 (ttm-80) REVERT: B 4695 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.6658 (mm110) outliers start: 25 outliers final: 14 residues processed: 74 average time/residue: 0.2128 time to fit residues: 20.8458 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 : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4409 ASN Chi-restraints excluded: chain A residue 4455 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4486 CYS Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4654 GLN Chi-restraints excluded: chain A residue 4699 LEU 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: 0.9990 chunk 36 optimal weight: 0.0970 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.100396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074567 restraints weight = 15942.594| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.81 r_work: 0.3125 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6594 Z= 0.219 Angle : 0.639 7.964 9022 Z= 0.322 Chirality : 0.047 0.195 1026 Planarity : 0.004 0.047 1168 Dihedral : 7.352 57.010 1202 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 2.56 % Allowed : 18.66 % 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: -0.91 (0.30), residues: 798 helix: 0.77 (0.62), residues: 80 sheet: -0.06 (0.39), residues: 174 loop : -1.05 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B4376 HIS 0.008 0.001 HIS B4611 PHE 0.012 0.001 PHE B4782 TYR 0.021 0.002 TYR B4551 ARG 0.002 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 66 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8535 (pmm) cc_final: 0.7986 (mmt) REVERT: A 4675 MET cc_start: 0.8731 (pmm) cc_final: 0.8223 (pmm) REVERT: A 4792 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8535 (pp) REVERT: B 4383 MET cc_start: 0.6996 (tpt) cc_final: 0.6778 (tpt) REVERT: B 4476 TYR cc_start: 0.6159 (m-80) cc_final: 0.5817 (m-80) REVERT: B 4525 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8700 (ttmm) REVERT: B 4695 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: B 4783 GLU cc_start: 0.7329 (pt0) cc_final: 0.6731 (tt0) outliers start: 18 outliers final: 10 residues processed: 62 average time/residue: 0.2284 time to fit residues: 18.3949 Evaluate side-chains 54 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 4744 GLU 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 4695 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 chunk 36 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.100312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074504 restraints weight = 15729.100| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.80 r_work: 0.3108 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6594 Z= 0.189 Angle : 0.615 8.284 9022 Z= 0.311 Chirality : 0.046 0.209 1026 Planarity : 0.004 0.046 1168 Dihedral : 6.424 55.888 1193 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.36 % Rotamer: Outliers : 2.99 % Allowed : 18.95 % Favored : 78.06 % 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: -0.91 (0.30), residues: 798 helix: 0.90 (0.63), residues: 80 sheet: -0.03 (0.39), residues: 174 loop : -1.09 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B4376 HIS 0.005 0.001 HIS A4477 PHE 0.014 0.001 PHE A4782 TYR 0.013 0.001 TYR A4476 ARG 0.005 0.000 ARG A4559 *********************** 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 65 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 4525 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8159 (ttmm) REVERT: A 4675 MET cc_start: 0.8613 (pmm) cc_final: 0.8034 (pmm) REVERT: A 4791 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7698 (t) REVERT: A 4792 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8510 (pp) REVERT: B 4415 ARG cc_start: 0.8938 (mtp180) cc_final: 0.8073 (mtp85) REVERT: B 4476 TYR cc_start: 0.6246 (m-80) cc_final: 0.5941 (m-80) REVERT: B 4525 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: B 4695 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7172 (mm110) REVERT: B 4783 GLU cc_start: 0.7617 (pt0) cc_final: 0.7051 (tt0) REVERT: B 4792 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8763 (pp) outliers start: 21 outliers final: 10 residues processed: 59 average time/residue: 0.2040 time to fit residues: 16.1699 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 : 0.637 ------------------------------------------------------------------------------- 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 4525 LYS Chi-restraints excluded: chain A residue 4548 LEU Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4699 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.0370 chunk 66 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.3472 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.100492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074704 restraints weight = 15597.339| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.78 r_work: 0.3114 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4432 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 : 0.601 7.721 9022 Z= 0.302 Chirality : 0.045 0.208 1026 Planarity : 0.004 0.044 1168 Dihedral : 5.858 54.957 1190 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.61 % Rotamer: Outliers : 4.13 % Allowed : 19.23 % 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 (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: -0.75 (0.30), residues: 798 helix: 1.99 (0.66), residues: 68 sheet: 0.07 (0.40), residues: 174 loop : -1.07 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B4376 HIS 0.003 0.001 HIS B4611 PHE 0.010 0.001 PHE A4782 TYR 0.014 0.001 TYR A4476 ARG 0.005 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 71 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8566 (pmm) cc_final: 0.7957 (mmt) REVERT: A 4675 MET cc_start: 0.8554 (pmm) cc_final: 0.7964 (pmm) REVERT: A 4753 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8366 (ppp) REVERT: A 4792 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8494 (pp) REVERT: B 4415 ARG cc_start: 0.8916 (mtp180) cc_final: 0.8071 (mtp85) REVERT: B 4476 TYR cc_start: 0.6310 (m-80) cc_final: 0.5998 (m-80) REVERT: B 4525 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8559 (ttmm) REVERT: B 4675 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8472 (ptp) REVERT: B 4695 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7193 (mm110) REVERT: B 4783 GLU cc_start: 0.7565 (pt0) cc_final: 0.7076 (tt0) REVERT: B 4792 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8733 (pp) outliers start: 29 outliers final: 12 residues processed: 64 average time/residue: 0.1893 time to fit residues: 16.5682 Evaluate side-chains 57 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 4584 CYS Chi-restraints excluded: chain A residue 4611 HIS Chi-restraints excluded: chain A residue 4699 LEU Chi-restraints excluded: chain A residue 4753 MET 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 4675 MET 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: 0.8980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.0010 chunk 70 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.099770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073938 restraints weight = 15673.603| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.77 r_work: 0.3096 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6594 Z= 0.199 Angle : 0.607 7.743 9022 Z= 0.307 Chirality : 0.045 0.210 1026 Planarity : 0.004 0.042 1168 Dihedral : 5.727 54.506 1190 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.71 % Allowed : 20.23 % 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 (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: 1.99 (0.66), residues: 68 sheet: 0.22 (0.40), residues: 172 loop : -1.09 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B4376 HIS 0.005 0.001 HIS B4477 PHE 0.012 0.001 PHE A4782 TYR 0.013 0.001 TYR A4476 ARG 0.004 0.000 ARG B4559 *********************** 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 61 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4415 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8125 (mtp85) REVERT: A 4507 MET cc_start: 0.8569 (pmm) cc_final: 0.7900 (mmt) REVERT: A 4675 MET cc_start: 0.8538 (pmm) cc_final: 0.7977 (pmm) REVERT: A 4753 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8404 (ppp) REVERT: A 4792 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8549 (pp) REVERT: B 4476 TYR cc_start: 0.6486 (m-80) cc_final: 0.6148 (m-80) REVERT: B 4525 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8566 (ttmm) REVERT: B 4675 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8398 (ptp) REVERT: B 4695 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7375 (mm110) REVERT: B 4783 GLU cc_start: 0.7903 (pt0) cc_final: 0.7462 (tt0) REVERT: B 4792 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8733 (pp) outliers start: 19 outliers final: 8 residues processed: 55 average time/residue: 0.1919 time to fit residues: 14.2513 Evaluate side-chains 53 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 4675 MET 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: 0.9980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.099071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073247 restraints weight = 15571.691| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.77 r_work: 0.3082 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6594 Z= 0.216 Angle : 0.613 6.537 9022 Z= 0.309 Chirality : 0.045 0.181 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.646 55.028 1190 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.70 % Allowed : 19.37 % Favored : 76.92 % 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: -0.65 (0.30), residues: 798 helix: 2.00 (0.66), residues: 68 sheet: 0.32 (0.40), residues: 172 loop : -1.05 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4376 HIS 0.004 0.001 HIS B4477 PHE 0.012 0.001 PHE A4782 TYR 0.013 0.001 TYR A4476 ARG 0.004 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 69 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4415 ARG cc_start: 0.8439 (mtp180) cc_final: 0.8118 (mtp85) REVERT: A 4507 MET cc_start: 0.8620 (pmm) cc_final: 0.8086 (mmt) REVERT: A 4525 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8426 (ttmm) REVERT: A 4609 LYS cc_start: 0.8545 (tttt) cc_final: 0.8326 (tttt) REVERT: A 4675 MET cc_start: 0.8505 (pmm) cc_final: 0.7970 (pmm) REVERT: A 4753 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8415 (ppp) REVERT: A 4792 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8523 (pp) REVERT: B 4476 TYR cc_start: 0.6453 (m-80) cc_final: 0.6081 (m-80) REVERT: B 4525 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8546 (ttmm) REVERT: B 4609 LYS cc_start: 0.7163 (ttpt) cc_final: 0.6654 (ttpt) REVERT: B 4675 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8378 (ptp) REVERT: B 4695 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7482 (mm110) REVERT: B 4783 GLU cc_start: 0.7643 (pt0) cc_final: 0.7156 (tt0) REVERT: B 4792 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8753 (pp) outliers start: 26 outliers final: 11 residues processed: 61 average time/residue: 0.2209 time to fit residues: 17.7773 Evaluate side-chains 62 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 4525 LYS Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4611 HIS 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 4467 ASP 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 4675 MET 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: 0.9980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 63 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.098630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072597 restraints weight = 15794.744| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.79 r_work: 0.3068 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6594 Z= 0.223 Angle : 0.610 6.647 9022 Z= 0.308 Chirality : 0.045 0.143 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.591 55.651 1190 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.56 % Allowed : 19.80 % 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: -0.69 (0.30), residues: 798 helix: 2.02 (0.66), residues: 68 sheet: 0.26 (0.40), residues: 174 loop : -1.08 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4376 HIS 0.003 0.001 HIS B4611 PHE 0.012 0.001 PHE B4782 TYR 0.013 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 62 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8691 (pmm) cc_final: 0.8089 (mmt) REVERT: A 4675 MET cc_start: 0.8546 (pmm) cc_final: 0.7949 (pmm) REVERT: A 4753 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8392 (ppp) REVERT: A 4792 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8535 (pp) REVERT: B 4476 TYR cc_start: 0.6547 (m-80) cc_final: 0.6088 (m-80) REVERT: B 4525 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8540 (ttmm) REVERT: B 4695 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7616 (mm110) REVERT: B 4783 GLU cc_start: 0.7952 (pt0) cc_final: 0.7526 (tt0) REVERT: B 4792 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8738 (pp) outliers start: 18 outliers final: 10 residues processed: 55 average time/residue: 0.2208 time to fit residues: 15.9575 Evaluate side-chains 56 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 4467 ASP 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: 0.9980 chunk 74 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 77 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.098774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072753 restraints weight = 15589.994| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.78 r_work: 0.3074 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6594 Z= 0.209 Angle : 0.609 7.062 9022 Z= 0.307 Chirality : 0.045 0.141 1026 Planarity : 0.004 0.041 1168 Dihedral : 5.495 56.376 1190 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.28 % Allowed : 20.09 % 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: -0.65 (0.30), residues: 798 helix: 2.00 (0.66), residues: 68 sheet: 0.43 (0.40), residues: 172 loop : -1.10 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A4426 HIS 0.006 0.001 HIS A4611 PHE 0.012 0.001 PHE A4782 TYR 0.010 0.001 TYR A4551 ARG 0.004 0.000 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 57 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4507 MET cc_start: 0.8651 (pmm) cc_final: 0.8172 (mmt) REVERT: A 4509 MET cc_start: 0.8263 (ptm) cc_final: 0.8020 (ptp) REVERT: A 4525 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8522 (ttmm) REVERT: A 4675 MET cc_start: 0.8555 (pmm) cc_final: 0.7956 (pmm) REVERT: A 4753 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8387 (ppp) REVERT: A 4792 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8515 (pp) REVERT: B 4476 TYR cc_start: 0.6541 (m-80) cc_final: 0.6137 (m-80) REVERT: B 4525 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8532 (ttmm) REVERT: B 4695 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7673 (mm110) REVERT: B 4783 GLU cc_start: 0.7941 (pt0) cc_final: 0.7587 (tt0) REVERT: B 4792 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8695 (pp) outliers start: 16 outliers final: 9 residues processed: 51 average time/residue: 0.2080 time to fit residues: 14.2625 Evaluate side-chains 56 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 4525 LYS Chi-restraints excluded: chain A residue 4584 CYS Chi-restraints excluded: chain A residue 4611 HIS 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 4467 ASP 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: 0.7980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.098635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072549 restraints weight = 15915.824| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.80 r_work: 0.3067 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6594 Z= 0.210 Angle : 0.605 7.559 9022 Z= 0.306 Chirality : 0.045 0.140 1026 Planarity : 0.004 0.040 1168 Dihedral : 5.442 56.967 1190 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 2.28 % Allowed : 20.37 % 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: -0.68 (0.30), residues: 798 helix: 2.03 (0.66), residues: 68 sheet: 0.36 (0.40), residues: 174 loop : -1.11 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B4376 HIS 0.005 0.001 HIS B4477 PHE 0.012 0.001 PHE A4782 TYR 0.010 0.001 TYR A4551 ARG 0.004 0.000 ARG A4559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3265.36 seconds wall clock time: 56 minutes 40.19 seconds (3400.19 seconds total)