Starting phenix.real_space_refine on Wed Jun 18 09:40:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sew_40431/06_2025/8sew_40431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sew_40431/06_2025/8sew_40431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sew_40431/06_2025/8sew_40431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sew_40431/06_2025/8sew_40431.map" model { file = "/net/cci-nas-00/data/ceres_data/8sew_40431/06_2025/8sew_40431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sew_40431/06_2025/8sew_40431.cif" } resolution = 2.89 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= -0.003 sd= 0.151 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 8 5.49 5 S 160 5.16 5 C 13448 2.51 5 N 3296 2.21 5 O 3800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20716 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5151 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4477 SG CYS A4958 57.159 83.295 88.728 1.00 36.39 S ATOM 4502 SG CYS A4961 59.556 83.860 91.636 1.00 36.10 S Restraints were copied for chains: C, B, D Time building chain proxies: 13.18, per 1000 atoms: 0.64 Number of scatterers: 20716 At special positions: 0 Unit cell: (145.544, 145.544, 133.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 160 16.00 P 8 15.00 O 3800 8.00 N 3296 7.00 C 13448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 78.1% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 3950 through 3970 removed outlier: 3.623A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A3960 " --> pdb=" O SER A3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3982 Processing helix chain 'A' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4225 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4558 through 4577 Processing helix chain 'A' and resid 4638 through 4665 Processing helix chain 'A' and resid 4665 through 4683 Processing helix chain 'A' and resid 4696 through 4703 Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4741 Processing helix chain 'A' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 Processing helix chain 'A' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 Processing helix chain 'A' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR A4863 " --> pdb=" O ARG A4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A4864 " --> pdb=" O LYS A4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4860 through 4864' Processing helix chain 'A' and resid 4878 through 4890 Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 4999 through 5003 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'A' and resid 5032 through 5037 Processing helix chain 'B' and resid 3951 through 3970 removed outlier: 3.554A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3982 Processing helix chain 'B' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4051 Processing helix chain 'B' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4225 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4558 through 4577 Processing helix chain 'B' and resid 4638 through 4665 Processing helix chain 'B' and resid 4665 through 4683 Processing helix chain 'B' and resid 4696 through 4703 Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4734 through 4741 Processing helix chain 'B' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B4750 " --> pdb=" O ALA B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4813 Processing helix chain 'B' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 Processing helix chain 'B' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B4864 " --> pdb=" O LYS B4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4860 through 4864' Processing helix chain 'B' and resid 4878 through 4890 Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 4999 through 5003 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'B' and resid 5032 through 5037 Processing helix chain 'C' and resid 3951 through 3970 removed outlier: 3.554A pdb=" N GLN C3960 " --> pdb=" O SER C3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3982 Processing helix chain 'C' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4225 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4558 through 4577 Processing helix chain 'C' and resid 4638 through 4665 Processing helix chain 'C' and resid 4665 through 4683 Processing helix chain 'C' and resid 4696 through 4703 Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4734 through 4741 Processing helix chain 'C' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE C4750 " --> pdb=" O ALA C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4813 Processing helix chain 'C' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 Processing helix chain 'C' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR C4863 " --> pdb=" O ARG C4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN C4864 " --> pdb=" O LYS C4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4860 through 4864' Processing helix chain 'C' and resid 4878 through 4890 Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 4999 through 5003 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'C' and resid 5032 through 5037 Processing helix chain 'D' and resid 3951 through 3970 removed outlier: 3.554A pdb=" N GLN D3960 " --> pdb=" O SER D3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3982 Processing helix chain 'D' and resid 3984 through 4006 removed outlier: 3.611A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4031 removed outlier: 3.621A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4051 Processing helix chain 'D' and resid 4051 through 4060 removed outlier: 3.680A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4225 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4558 through 4577 Processing helix chain 'D' and resid 4638 through 4665 Processing helix chain 'D' and resid 4665 through 4683 Processing helix chain 'D' and resid 4696 through 4703 Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.226A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4734 through 4741 Processing helix chain 'D' and resid 4744 through 4750 removed outlier: 4.005A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE D4750 " --> pdb=" O ALA D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.983A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 Processing helix chain 'D' and resid 4814 through 4820 removed outlier: 4.144A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.784A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 Processing helix chain 'D' and resid 4860 through 4864 removed outlier: 3.571A pdb=" N TYR D4863 " --> pdb=" O ARG D4860 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN D4864 " --> pdb=" O LYS D4861 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4860 through 4864' Processing helix chain 'D' and resid 4878 through 4890 Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4926 through 4957 removed outlier: 4.134A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 3.938A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 4999 through 5003 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing helix chain 'D' and resid 5032 through 5037 Processing sheet with id=AA1, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id=AA3, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AA4, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AA5, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id=AA6, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id=AA7, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4583 1388 hydrogen bonds defined for protein. 4068 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: 7.02 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6512 1.34 - 1.46: 4856 1.46 - 1.58: 9552 1.58 - 1.69: 12 1.69 - 1.81: 276 Bond restraints: 21208 Sorted by residual: bond pdb=" C4 ADP B5101 " pdb=" C5 ADP B5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP C5101 " pdb=" C5 ADP C5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP A5101 " pdb=" C5 ADP A5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP D5101 " pdb=" C5 ADP D5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C5 ADP A5101 " pdb=" C6 ADP A5101 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.87e+01 ... (remaining 21203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 28460 2.75 - 5.49: 140 5.49 - 8.24: 28 8.24 - 10.99: 12 10.99 - 13.74: 4 Bond angle restraints: 28644 Sorted by residual: angle pdb=" C LYS A4665 " pdb=" N VAL A4666 " pdb=" CA VAL A4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS B4665 " pdb=" N VAL B4666 " pdb=" CA VAL B4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS D4665 " pdb=" N VAL D4666 " pdb=" CA VAL D4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS C4665 " pdb=" N VAL C4666 " pdb=" CA VAL C4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" PA ADP C5101 " pdb=" O3A ADP C5101 " pdb=" PB ADP C5101 " ideal model delta sigma weight residual 120.50 134.24 -13.74 3.00e+00 1.11e-01 2.10e+01 ... (remaining 28639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.20: 12212 30.20 - 60.41: 228 60.41 - 90.61: 12 90.61 - 120.81: 4 120.81 - 151.01: 4 Dihedral angle restraints: 12460 sinusoidal: 5112 harmonic: 7348 Sorted by residual: dihedral pdb=" C2' ADP A5101 " pdb=" C1' ADP A5101 " pdb=" N9 ADP A5101 " pdb=" C4 ADP A5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C2' ADP D5101 " pdb=" C1' ADP D5101 " pdb=" N9 ADP D5101 " pdb=" C4 ADP D5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C2' ADP C5101 " pdb=" C1' ADP C5101 " pdb=" N9 ADP C5101 " pdb=" C4 ADP C5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 12457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1724 0.029 - 0.058: 1004 0.058 - 0.087: 288 0.087 - 0.116: 68 0.116 - 0.144: 12 Chirality restraints: 3096 Sorted by residual: chirality pdb=" C3' ADP C5101 " pdb=" C2' ADP C5101 " pdb=" C4' ADP C5101 " pdb=" O3' ADP C5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C3' ADP D5101 " pdb=" C2' ADP D5101 " pdb=" C4' ADP D5101 " pdb=" O3' ADP D5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C3' ADP A5101 " pdb=" C2' ADP A5101 " pdb=" C4' ADP A5101 " pdb=" O3' ADP A5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3093 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B4913 " 0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG B4913 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B4913 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B4913 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B4913 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A4913 " -0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG A4913 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A4913 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A4913 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A4913 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D4913 " -0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG D4913 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D4913 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D4913 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D4913 " -0.006 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.19: 12 1.19 - 2.12: 24 2.12 - 3.05: 13632 3.05 - 3.97: 54820 3.97 - 4.90: 102550 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171038 Sorted by model distance: nonbonded pdb=" NH2 ARG B4944 " pdb=" OD1 ASP C4938 " model vdw 0.267 3.120 nonbonded pdb=" NH2 ARG C4944 " pdb=" OD1 ASP D4938 " model vdw 0.267 3.120 nonbonded pdb=" OD1 ASP A4938 " pdb=" NH2 ARG D4944 " model vdw 0.267 3.120 nonbonded pdb=" NH2 ARG A4944 " pdb=" OD1 ASP B4938 " model vdw 0.267 3.120 nonbonded pdb=" OE2 GLU A4976 " pdb=" OE2 GLU B4227 " model vdw 0.697 3.040 ... (remaining 171033 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 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: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 53.160 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.014 0.990 21232 Z= 1.374 Angle : 0.595 13.737 28660 Z= 0.295 Chirality : 0.038 0.144 3096 Planarity : 0.004 0.056 3612 Dihedral : 12.563 151.014 7712 Min Nonbonded Distance : 0.267 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 2.14 % Allowed : 4.28 % Favored : 93.58 % 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: 1.93 (0.17), residues: 2476 helix: 1.99 (0.12), residues: 1644 sheet: 0.31 (0.51), residues: 112 loop : -0.16 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C5019 HIS 0.005 0.001 HIS D4886 PHE 0.020 0.002 PHE C4916 TYR 0.012 0.001 TYR C4994 ARG 0.003 0.001 ARG C4913 Details of bonding type rmsd hydrogen bonds : bond 0.14631 ( 1388) hydrogen bonds : angle 4.68462 ( 4068) metal coordination : bond 0.01221 ( 16) metal coordination : angle 4.26074 ( 8) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.90757 ( 8) covalent geometry : bond 0.00432 (21208) covalent geometry : angle 0.59063 (28644) Misc. bond : bond 0.99042 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 464 time to evaluate : 2.259 Fit side-chains REVERT: A 3992 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: A 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: A 4580 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6354 (t80) REVERT: A 4644 TRP cc_start: 0.7187 (t60) cc_final: 0.6975 (t-100) REVERT: A 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6792 (m-30) REVERT: A 4844 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 3992 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: B 4196 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: B 4580 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6353 (t80) REVERT: B 4644 TRP cc_start: 0.7185 (t60) cc_final: 0.6971 (t-100) REVERT: B 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6788 (m-30) REVERT: B 4844 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (tp) REVERT: C 3992 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: C 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5992 (tp30) REVERT: C 4580 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6347 (t80) REVERT: C 4644 TRP cc_start: 0.7186 (t60) cc_final: 0.6975 (t-100) REVERT: C 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6790 (m-30) REVERT: C 4844 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8091 (tp) REVERT: D 3992 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: D 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5991 (tp30) REVERT: D 4580 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6348 (t80) REVERT: D 4644 TRP cc_start: 0.7186 (t60) cc_final: 0.6975 (t-100) REVERT: D 4726 ASP cc_start: 0.7011 (m-30) cc_final: 0.6792 (m-30) REVERT: D 4844 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8094 (tp) outliers start: 48 outliers final: 16 residues processed: 508 average time/residue: 1.3186 time to fit residues: 760.7460 Evaluate side-chains 396 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3992 PHE Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain B residue 3992 PHE Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain C residue 3992 PHE Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain D residue 3992 PHE Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 118 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4973 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4973 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4973 HIS ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.174679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140988 restraints weight = 24365.160| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.96 r_work: 0.3339 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21232 Z= 0.132 Angle : 0.602 13.465 28660 Z= 0.299 Chirality : 0.038 0.141 3096 Planarity : 0.004 0.049 3612 Dihedral : 10.041 144.150 2812 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 3.39 % Allowed : 12.83 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.17), residues: 2476 helix: 2.16 (0.12), residues: 1700 sheet: 0.07 (0.49), residues: 112 loop : 0.03 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D3986 HIS 0.004 0.001 HIS C3994 PHE 0.018 0.001 PHE D4916 TYR 0.010 0.001 TYR D5032 ARG 0.008 0.001 ARG D4189 Details of bonding type rmsd hydrogen bonds : bond 0.04915 ( 1388) hydrogen bonds : angle 4.09876 ( 4068) metal coordination : bond 0.00318 ( 16) metal coordination : angle 3.66686 ( 8) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.90254 ( 8) covalent geometry : bond 0.00276 (21208) covalent geometry : angle 0.59934 (28644) Misc. bond : bond 0.00197 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 396 time to evaluate : 2.299 Fit side-chains REVERT: A 4023 MET cc_start: 0.7539 (ttp) cc_final: 0.6938 (tpp) REVERT: A 4042 ARG cc_start: 0.6722 (mtm110) cc_final: 0.6108 (mtm180) REVERT: A 4184 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8025 (ttp) REVERT: A 4196 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5936 (tp30) REVERT: A 4580 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6499 (t80) REVERT: A 4584 ASP cc_start: 0.6695 (t0) cc_final: 0.6475 (p0) REVERT: A 4644 TRP cc_start: 0.7702 (t60) cc_final: 0.7414 (t-100) REVERT: A 4726 ASP cc_start: 0.7329 (m-30) cc_final: 0.7067 (m-30) REVERT: A 4992 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8381 (mt) REVERT: B 4023 MET cc_start: 0.7521 (ttp) cc_final: 0.6916 (tpp) REVERT: B 4042 ARG cc_start: 0.6734 (mtm110) cc_final: 0.6118 (mtm180) REVERT: B 4184 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8016 (ttp) REVERT: B 4196 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5932 (tp30) REVERT: B 4580 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6504 (t80) REVERT: B 4584 ASP cc_start: 0.6701 (t0) cc_final: 0.6486 (p0) REVERT: B 4644 TRP cc_start: 0.7696 (t60) cc_final: 0.7408 (t-100) REVERT: B 4726 ASP cc_start: 0.7329 (m-30) cc_final: 0.7064 (m-30) REVERT: B 4992 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8380 (mt) REVERT: C 4023 MET cc_start: 0.7513 (ttp) cc_final: 0.6912 (tpp) REVERT: C 4042 ARG cc_start: 0.6737 (mtm110) cc_final: 0.6118 (mtm180) REVERT: C 4184 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: C 4196 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5938 (tp30) REVERT: C 4580 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6504 (t80) REVERT: C 4584 ASP cc_start: 0.6702 (t0) cc_final: 0.6481 (p0) REVERT: C 4644 TRP cc_start: 0.7696 (t60) cc_final: 0.7408 (t-100) REVERT: C 4726 ASP cc_start: 0.7329 (m-30) cc_final: 0.7068 (m-30) REVERT: C 4992 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8369 (mt) REVERT: D 4023 MET cc_start: 0.7519 (ttp) cc_final: 0.6915 (tpp) REVERT: D 4042 ARG cc_start: 0.6738 (mtm110) cc_final: 0.6122 (mtm180) REVERT: D 4184 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8007 (ttp) REVERT: D 4196 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.5935 (tp30) REVERT: D 4580 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6516 (t80) REVERT: D 4584 ASP cc_start: 0.6698 (t0) cc_final: 0.6476 (p0) REVERT: D 4644 TRP cc_start: 0.7703 (t60) cc_final: 0.7410 (t-100) REVERT: D 4726 ASP cc_start: 0.7322 (m-30) cc_final: 0.7059 (m-30) REVERT: D 4992 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8375 (mt) outliers start: 76 outliers final: 16 residues processed: 432 average time/residue: 1.3376 time to fit residues: 651.9952 Evaluate side-chains 404 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 185 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS A5031 GLN B4973 HIS B5031 GLN C4973 HIS C5031 GLN D4973 HIS D5031 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.173781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140125 restraints weight = 24241.011| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.13 r_work: 0.3328 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21232 Z= 0.143 Angle : 0.580 12.717 28660 Z= 0.288 Chirality : 0.038 0.134 3096 Planarity : 0.004 0.055 3612 Dihedral : 9.548 145.616 2784 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 4.10 % Allowed : 13.90 % Favored : 82.00 % 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: 2.23 (0.17), residues: 2476 helix: 2.16 (0.12), residues: 1704 sheet: -0.27 (0.48), residues: 112 loop : 0.05 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B5019 HIS 0.004 0.001 HIS A3994 PHE 0.019 0.001 PHE A4916 TYR 0.013 0.001 TYR D5032 ARG 0.008 0.001 ARG D4736 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 1388) hydrogen bonds : angle 4.10891 ( 4068) metal coordination : bond 0.00763 ( 16) metal coordination : angle 4.02206 ( 8) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.19191 ( 8) covalent geometry : bond 0.00320 (21208) covalent geometry : angle 0.57560 (28644) Misc. bond : bond 0.00385 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 384 time to evaluate : 2.285 Fit side-chains REVERT: A 3955 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7028 (mtm) REVERT: A 3992 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: A 4023 MET cc_start: 0.7501 (ttp) cc_final: 0.6997 (tpp) REVERT: A 4042 ARG cc_start: 0.6589 (mtm110) cc_final: 0.5932 (mtm180) REVERT: A 4184 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: A 4196 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5985 (tp30) REVERT: A 4209 GLN cc_start: 0.7985 (pt0) cc_final: 0.7481 (pm20) REVERT: A 4212 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 4224 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: A 4580 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6587 (t80) REVERT: A 4584 ASP cc_start: 0.6840 (t0) cc_final: 0.6555 (p0) REVERT: A 4644 TRP cc_start: 0.7731 (t60) cc_final: 0.7454 (t-100) REVERT: A 4726 ASP cc_start: 0.7304 (m-30) cc_final: 0.7080 (m-30) REVERT: A 4911 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (mm) REVERT: A 4992 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 3955 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7034 (mtm) REVERT: B 3992 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: B 4023 MET cc_start: 0.7495 (ttp) cc_final: 0.6989 (tpp) REVERT: B 4042 ARG cc_start: 0.6586 (mtm110) cc_final: 0.5925 (mtm180) REVERT: B 4184 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: B 4196 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5988 (tp30) REVERT: B 4209 GLN cc_start: 0.7991 (pt0) cc_final: 0.7492 (pm20) REVERT: B 4212 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: B 4224 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: B 4580 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.6584 (t80) REVERT: B 4584 ASP cc_start: 0.6847 (t0) cc_final: 0.6561 (p0) REVERT: B 4644 TRP cc_start: 0.7729 (t60) cc_final: 0.7450 (t-100) REVERT: B 4726 ASP cc_start: 0.7306 (m-30) cc_final: 0.7085 (m-30) REVERT: B 4911 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7632 (mm) REVERT: B 4992 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 3955 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7042 (mtm) REVERT: C 3992 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: C 4015 GLU cc_start: 0.7089 (tt0) cc_final: 0.6888 (mp0) REVERT: C 4023 MET cc_start: 0.7477 (ttp) cc_final: 0.6969 (tpp) REVERT: C 4042 ARG cc_start: 0.6606 (mtm110) cc_final: 0.5944 (mtm180) REVERT: C 4184 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8089 (ttp) REVERT: C 4196 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5992 (tp30) REVERT: C 4209 GLN cc_start: 0.7983 (pt0) cc_final: 0.7478 (pm20) REVERT: C 4212 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: C 4224 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: C 4580 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6592 (t80) REVERT: C 4584 ASP cc_start: 0.6849 (t0) cc_final: 0.6567 (p0) REVERT: C 4644 TRP cc_start: 0.7728 (t60) cc_final: 0.7449 (t-100) REVERT: C 4726 ASP cc_start: 0.7304 (m-30) cc_final: 0.7084 (m-30) REVERT: C 4992 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8417 (mt) REVERT: D 3955 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7043 (mtm) REVERT: D 3992 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: D 4015 GLU cc_start: 0.7084 (tt0) cc_final: 0.6883 (mp0) REVERT: D 4023 MET cc_start: 0.7485 (ttp) cc_final: 0.6982 (tpp) REVERT: D 4042 ARG cc_start: 0.6609 (mtm110) cc_final: 0.5951 (mtm180) REVERT: D 4184 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8073 (ttp) REVERT: D 4196 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5974 (tp30) REVERT: D 4209 GLN cc_start: 0.7973 (pt0) cc_final: 0.7463 (pm20) REVERT: D 4212 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: D 4224 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: D 4580 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6594 (t80) REVERT: D 4584 ASP cc_start: 0.6836 (t0) cc_final: 0.6557 (p0) REVERT: D 4644 TRP cc_start: 0.7733 (t60) cc_final: 0.7451 (t-100) REVERT: D 4726 ASP cc_start: 0.7309 (m-30) cc_final: 0.7084 (m-30) REVERT: D 4911 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7632 (mm) REVERT: D 4992 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8421 (mt) outliers start: 92 outliers final: 24 residues processed: 428 average time/residue: 1.4065 time to fit residues: 677.9770 Evaluate side-chains 418 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 359 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 3992 PHE Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 3992 PHE Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3955 MET Chi-restraints excluded: chain C residue 3992 PHE Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3955 MET Chi-restraints excluded: chain D residue 3992 PHE Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 165 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 237 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4043 GLN A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138552 restraints weight = 24579.371| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.15 r_work: 0.3310 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21232 Z= 0.194 Angle : 0.606 7.345 28660 Z= 0.305 Chirality : 0.040 0.137 3096 Planarity : 0.004 0.065 3612 Dihedral : 9.511 148.224 2784 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 4.50 % Allowed : 14.39 % Favored : 81.11 % 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: 2.00 (0.17), residues: 2476 helix: 1.95 (0.12), residues: 1704 sheet: 0.63 (0.67), residues: 64 loop : -0.08 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A5019 HIS 0.004 0.001 HIS A4886 PHE 0.022 0.002 PHE B4916 TYR 0.011 0.002 TYR B4994 ARG 0.010 0.001 ARG B4189 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 1388) hydrogen bonds : angle 4.29445 ( 4068) metal coordination : bond 0.01307 ( 16) metal coordination : angle 4.62778 ( 8) SS BOND : bond 0.00300 ( 4) SS BOND : angle 1.41168 ( 8) covalent geometry : bond 0.00455 (21208) covalent geometry : angle 0.60067 (28644) Misc. bond : bond 0.00445 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 371 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3955 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7062 (mtm) REVERT: A 3959 LYS cc_start: 0.6368 (tttp) cc_final: 0.6023 (tttp) REVERT: A 3980 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7775 (mm) REVERT: A 4022 ASP cc_start: 0.6387 (m-30) cc_final: 0.6185 (m-30) REVERT: A 4023 MET cc_start: 0.7531 (ttp) cc_final: 0.7193 (tpp) REVERT: A 4042 ARG cc_start: 0.6608 (mtm110) cc_final: 0.5969 (mtm180) REVERT: A 4196 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6063 (tp30) REVERT: A 4209 GLN cc_start: 0.8060 (pt0) cc_final: 0.7540 (pm20) REVERT: A 4212 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: A 4580 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 4584 ASP cc_start: 0.6881 (t0) cc_final: 0.6669 (p0) REVERT: A 4644 TRP cc_start: 0.7725 (t60) cc_final: 0.7429 (t-100) REVERT: A 4726 ASP cc_start: 0.7309 (m-30) cc_final: 0.7081 (m-30) REVERT: A 4887 MET cc_start: 0.8368 (mmm) cc_final: 0.8045 (tpt) REVERT: A 4911 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7671 (mm) REVERT: B 3955 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7063 (mtm) REVERT: B 3959 LYS cc_start: 0.6351 (tttp) cc_final: 0.6045 (tttp) REVERT: B 3980 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7774 (mm) REVERT: B 4023 MET cc_start: 0.7524 (ttp) cc_final: 0.7184 (tpp) REVERT: B 4039 MET cc_start: 0.7797 (mtp) cc_final: 0.7370 (ttm) REVERT: B 4042 ARG cc_start: 0.6610 (mtm110) cc_final: 0.5955 (mtm180) REVERT: B 4196 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6067 (tp30) REVERT: B 4209 GLN cc_start: 0.8073 (pt0) cc_final: 0.7552 (pm20) REVERT: B 4212 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: B 4580 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6688 (t80) REVERT: B 4584 ASP cc_start: 0.6879 (t0) cc_final: 0.6669 (p0) REVERT: B 4644 TRP cc_start: 0.7725 (t60) cc_final: 0.7430 (t-100) REVERT: B 4726 ASP cc_start: 0.7310 (m-30) cc_final: 0.7083 (m-30) REVERT: B 4887 MET cc_start: 0.8348 (mmm) cc_final: 0.8037 (tpt) REVERT: B 4911 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7678 (mm) REVERT: C 3955 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7057 (mtm) REVERT: C 3959 LYS cc_start: 0.6344 (tttp) cc_final: 0.6046 (tttp) REVERT: C 3980 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7770 (mm) REVERT: C 4023 MET cc_start: 0.7502 (ttp) cc_final: 0.7160 (tpp) REVERT: C 4039 MET cc_start: 0.7774 (mtp) cc_final: 0.7359 (ttm) REVERT: C 4042 ARG cc_start: 0.6606 (mtm110) cc_final: 0.5954 (mtm180) REVERT: C 4196 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6062 (tp30) REVERT: C 4209 GLN cc_start: 0.8072 (pt0) cc_final: 0.7546 (pm20) REVERT: C 4212 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: C 4580 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6693 (t80) REVERT: C 4584 ASP cc_start: 0.6885 (t0) cc_final: 0.6675 (p0) REVERT: C 4644 TRP cc_start: 0.7733 (t60) cc_final: 0.7435 (t-100) REVERT: C 4726 ASP cc_start: 0.7304 (m-30) cc_final: 0.7077 (m-30) REVERT: C 4887 MET cc_start: 0.8356 (mmm) cc_final: 0.8041 (tpt) REVERT: D 3955 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7057 (mtm) REVERT: D 3959 LYS cc_start: 0.6347 (tttp) cc_final: 0.6045 (tttp) REVERT: D 3980 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7774 (mm) REVERT: D 4023 MET cc_start: 0.7517 (ttp) cc_final: 0.7178 (tpp) REVERT: D 4039 MET cc_start: 0.7795 (mtp) cc_final: 0.7366 (ttm) REVERT: D 4042 ARG cc_start: 0.6620 (mtm110) cc_final: 0.5968 (mtm180) REVERT: D 4196 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6054 (tp30) REVERT: D 4209 GLN cc_start: 0.8055 (pt0) cc_final: 0.7525 (pm20) REVERT: D 4212 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: D 4580 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6696 (t80) REVERT: D 4584 ASP cc_start: 0.6882 (t0) cc_final: 0.6668 (p0) REVERT: D 4644 TRP cc_start: 0.7731 (t60) cc_final: 0.7431 (t-100) REVERT: D 4726 ASP cc_start: 0.7307 (m-30) cc_final: 0.7078 (m-30) REVERT: D 4887 MET cc_start: 0.8371 (mmm) cc_final: 0.8054 (tpt) REVERT: D 4911 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7683 (mm) outliers start: 101 outliers final: 32 residues processed: 421 average time/residue: 1.2465 time to fit residues: 595.8552 Evaluate side-chains 416 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 3980 LEU Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4773 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 3980 LEU Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4773 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3955 MET Chi-restraints excluded: chain C residue 3980 LEU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4773 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3955 MET Chi-restraints excluded: chain D residue 3980 LEU Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4773 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 18 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4043 GLN B4973 HIS C4043 GLN C4973 HIS D4043 GLN D4973 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140206 restraints weight = 24679.620| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.14 r_work: 0.3329 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21232 Z= 0.142 Angle : 0.578 8.904 28660 Z= 0.288 Chirality : 0.038 0.134 3096 Planarity : 0.004 0.079 3612 Dihedral : 9.270 148.598 2776 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 3.74 % Allowed : 15.51 % Favored : 80.75 % 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: 2.11 (0.17), residues: 2476 helix: 2.06 (0.12), residues: 1704 sheet: 0.51 (0.67), residues: 64 loop : -0.10 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.003 0.001 HIS C4886 PHE 0.020 0.001 PHE B4916 TYR 0.009 0.001 TYR B4994 ARG 0.011 0.001 ARG D4736 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 1388) hydrogen bonds : angle 4.23056 ( 4068) metal coordination : bond 0.00574 ( 16) metal coordination : angle 4.10004 ( 8) SS BOND : bond 0.00236 ( 4) SS BOND : angle 1.33139 ( 8) covalent geometry : bond 0.00324 (21208) covalent geometry : angle 0.57407 (28644) Misc. bond : bond 0.00549 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 384 time to evaluate : 2.270 Fit side-chains REVERT: A 3955 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7081 (mtm) REVERT: A 3959 LYS cc_start: 0.6313 (tttp) cc_final: 0.5991 (tttp) REVERT: A 3986 TRP cc_start: 0.8405 (m100) cc_final: 0.7782 (m100) REVERT: A 3999 MET cc_start: 0.8217 (mmm) cc_final: 0.7830 (tpt) REVERT: A 4023 MET cc_start: 0.7403 (ttp) cc_final: 0.6930 (ttt) REVERT: A 4042 ARG cc_start: 0.6513 (mtm110) cc_final: 0.5783 (mtm180) REVERT: A 4054 ASN cc_start: 0.7345 (m110) cc_final: 0.7133 (m-40) REVERT: A 4196 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5849 (tp30) REVERT: A 4209 GLN cc_start: 0.8029 (pt0) cc_final: 0.7514 (pm20) REVERT: A 4212 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: A 4580 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6513 (t80) REVERT: A 4584 ASP cc_start: 0.6965 (t0) cc_final: 0.6719 (p0) REVERT: A 4644 TRP cc_start: 0.7764 (t60) cc_final: 0.7467 (t-100) REVERT: A 4704 LEU cc_start: 0.8953 (tp) cc_final: 0.8345 (mm) REVERT: A 4726 ASP cc_start: 0.7316 (m-30) cc_final: 0.7073 (m-30) REVERT: A 4887 MET cc_start: 0.8337 (mmm) cc_final: 0.8072 (tpt) REVERT: A 4911 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7651 (mm) REVERT: A 4992 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 3955 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7085 (mtm) REVERT: B 3959 LYS cc_start: 0.6287 (tttp) cc_final: 0.5976 (tttp) REVERT: B 3986 TRP cc_start: 0.8425 (m100) cc_final: 0.7801 (m100) REVERT: B 3999 MET cc_start: 0.8217 (mmm) cc_final: 0.7835 (tpt) REVERT: B 4023 MET cc_start: 0.7389 (ttp) cc_final: 0.6911 (ttt) REVERT: B 4042 ARG cc_start: 0.6519 (mtm110) cc_final: 0.5787 (mtm180) REVERT: B 4054 ASN cc_start: 0.7342 (m110) cc_final: 0.7136 (m-40) REVERT: B 4196 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5850 (tp30) REVERT: B 4209 GLN cc_start: 0.8038 (pt0) cc_final: 0.7525 (pm20) REVERT: B 4212 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: B 4580 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6515 (t80) REVERT: B 4584 ASP cc_start: 0.6977 (t0) cc_final: 0.6728 (p0) REVERT: B 4644 TRP cc_start: 0.7763 (t60) cc_final: 0.7467 (t-100) REVERT: B 4704 LEU cc_start: 0.8954 (tp) cc_final: 0.8348 (mm) REVERT: B 4726 ASP cc_start: 0.7323 (m-30) cc_final: 0.7076 (m-30) REVERT: B 4887 MET cc_start: 0.8309 (mmm) cc_final: 0.8048 (tpt) REVERT: B 4911 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7657 (mm) REVERT: B 4992 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8458 (mt) REVERT: C 3955 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7147 (mtm) REVERT: C 3959 LYS cc_start: 0.6288 (tttp) cc_final: 0.5980 (tttp) REVERT: C 3986 TRP cc_start: 0.8414 (m100) cc_final: 0.7798 (m100) REVERT: C 3999 MET cc_start: 0.8182 (mmm) cc_final: 0.7791 (tpt) REVERT: C 4023 MET cc_start: 0.7383 (ttp) cc_final: 0.6910 (ttt) REVERT: C 4042 ARG cc_start: 0.6525 (mtm110) cc_final: 0.5793 (mtm180) REVERT: C 4054 ASN cc_start: 0.7342 (m110) cc_final: 0.7133 (m-40) REVERT: C 4196 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5850 (tp30) REVERT: C 4209 GLN cc_start: 0.8044 (pt0) cc_final: 0.7524 (pm20) REVERT: C 4212 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: C 4580 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6513 (t80) REVERT: C 4584 ASP cc_start: 0.6963 (t0) cc_final: 0.6725 (p0) REVERT: C 4644 TRP cc_start: 0.7769 (t60) cc_final: 0.7473 (t-100) REVERT: C 4704 LEU cc_start: 0.8956 (tp) cc_final: 0.8356 (mm) REVERT: C 4726 ASP cc_start: 0.7313 (m-30) cc_final: 0.7071 (m-30) REVERT: C 4887 MET cc_start: 0.8309 (mmm) cc_final: 0.8052 (tpt) REVERT: C 4911 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7642 (mm) REVERT: C 4992 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8445 (mt) REVERT: D 3955 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7144 (mtm) REVERT: D 3959 LYS cc_start: 0.6292 (tttp) cc_final: 0.5980 (tttp) REVERT: D 3986 TRP cc_start: 0.8417 (m100) cc_final: 0.7800 (m100) REVERT: D 3999 MET cc_start: 0.8175 (mmm) cc_final: 0.7776 (tpt) REVERT: D 4023 MET cc_start: 0.7396 (ttp) cc_final: 0.6923 (ttt) REVERT: D 4042 ARG cc_start: 0.6522 (mtm110) cc_final: 0.5792 (mtm180) REVERT: D 4054 ASN cc_start: 0.7341 (m110) cc_final: 0.7130 (m-40) REVERT: D 4196 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5834 (tp30) REVERT: D 4209 GLN cc_start: 0.8029 (pt0) cc_final: 0.7504 (pm20) REVERT: D 4212 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: D 4580 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.6511 (t80) REVERT: D 4584 ASP cc_start: 0.6956 (t0) cc_final: 0.6716 (p0) REVERT: D 4644 TRP cc_start: 0.7768 (t60) cc_final: 0.7469 (t-100) REVERT: D 4704 LEU cc_start: 0.8956 (tp) cc_final: 0.8351 (mm) REVERT: D 4726 ASP cc_start: 0.7316 (m-30) cc_final: 0.7072 (m-30) REVERT: D 4887 MET cc_start: 0.8326 (mmm) cc_final: 0.8070 (tpt) REVERT: D 4911 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7654 (mm) REVERT: D 4992 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8444 (mt) outliers start: 84 outliers final: 24 residues processed: 436 average time/residue: 1.2831 time to fit residues: 634.2143 Evaluate side-chains 410 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 362 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3955 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3955 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3955 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 205 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 64 optimal weight: 0.0770 chunk 178 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.175511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142150 restraints weight = 24476.803| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.94 r_work: 0.3365 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21232 Z= 0.122 Angle : 0.597 12.899 28660 Z= 0.291 Chirality : 0.037 0.145 3096 Planarity : 0.004 0.077 3612 Dihedral : 9.126 148.518 2776 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 2.45 % Allowed : 17.34 % Favored : 80.21 % 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: 2.26 (0.17), residues: 2476 helix: 2.21 (0.12), residues: 1720 sheet: 0.42 (0.68), residues: 64 loop : -0.21 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.003 0.001 HIS D3994 PHE 0.020 0.001 PHE C4922 TYR 0.012 0.001 TYR B4580 ARG 0.012 0.001 ARG D4736 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 1388) hydrogen bonds : angle 4.14746 ( 4068) metal coordination : bond 0.00184 ( 16) metal coordination : angle 3.60038 ( 8) SS BOND : bond 0.00132 ( 4) SS BOND : angle 1.13479 ( 8) covalent geometry : bond 0.00270 (21208) covalent geometry : angle 0.59361 (28644) Misc. bond : bond 0.00641 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 384 time to evaluate : 2.302 Fit side-chains REVERT: A 3955 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7082 (mtm) REVERT: A 3959 LYS cc_start: 0.6205 (tttp) cc_final: 0.5907 (tttp) REVERT: A 3986 TRP cc_start: 0.8330 (m100) cc_final: 0.7787 (m100) REVERT: A 4023 MET cc_start: 0.7061 (ttp) cc_final: 0.6665 (ttt) REVERT: A 4042 ARG cc_start: 0.6468 (mtm110) cc_final: 0.5750 (mtm180) REVERT: A 4196 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5876 (tp30) REVERT: A 4199 GLU cc_start: 0.7620 (pm20) cc_final: 0.7146 (tp30) REVERT: A 4209 GLN cc_start: 0.7955 (pt0) cc_final: 0.7452 (pm20) REVERT: A 4212 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 4580 TYR cc_start: 0.6903 (t80) cc_final: 0.6392 (t80) REVERT: A 4584 ASP cc_start: 0.6727 (t0) cc_final: 0.6389 (p0) REVERT: A 4644 TRP cc_start: 0.7621 (t60) cc_final: 0.7304 (t-100) REVERT: A 4704 LEU cc_start: 0.8949 (tp) cc_final: 0.8321 (mm) REVERT: A 4726 ASP cc_start: 0.7311 (m-30) cc_final: 0.7058 (m-30) REVERT: A 4887 MET cc_start: 0.8387 (mmm) cc_final: 0.8081 (tpt) REVERT: A 4992 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 3959 LYS cc_start: 0.6182 (tttp) cc_final: 0.5896 (tttp) REVERT: B 3986 TRP cc_start: 0.8337 (m100) cc_final: 0.7793 (m100) REVERT: B 4023 MET cc_start: 0.7050 (ttp) cc_final: 0.6655 (ttt) REVERT: B 4042 ARG cc_start: 0.6483 (mtm110) cc_final: 0.5757 (mtm180) REVERT: B 4196 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.5871 (tp30) REVERT: B 4199 GLU cc_start: 0.7611 (pm20) cc_final: 0.7139 (tp30) REVERT: B 4209 GLN cc_start: 0.7962 (pt0) cc_final: 0.7460 (pm20) REVERT: B 4212 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: B 4580 TYR cc_start: 0.6898 (t80) cc_final: 0.6387 (t80) REVERT: B 4584 ASP cc_start: 0.6738 (t0) cc_final: 0.6395 (p0) REVERT: B 4644 TRP cc_start: 0.7621 (t60) cc_final: 0.7304 (t-100) REVERT: B 4704 LEU cc_start: 0.8950 (tp) cc_final: 0.8326 (mm) REVERT: B 4726 ASP cc_start: 0.7325 (m-30) cc_final: 0.7069 (m-30) REVERT: B 4887 MET cc_start: 0.8373 (mmm) cc_final: 0.8071 (tpt) REVERT: B 4992 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 3955 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7074 (mtm) REVERT: C 3959 LYS cc_start: 0.6207 (tttp) cc_final: 0.5926 (tttp) REVERT: C 3986 TRP cc_start: 0.8344 (m100) cc_final: 0.7808 (m100) REVERT: C 4023 MET cc_start: 0.7033 (ttp) cc_final: 0.6644 (ttt) REVERT: C 4042 ARG cc_start: 0.6490 (mtm110) cc_final: 0.5767 (mtm180) REVERT: C 4196 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5869 (tp30) REVERT: C 4199 GLU cc_start: 0.7613 (pm20) cc_final: 0.7140 (tp30) REVERT: C 4209 GLN cc_start: 0.7965 (pt0) cc_final: 0.7454 (pm20) REVERT: C 4212 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: C 4580 TYR cc_start: 0.6888 (t80) cc_final: 0.6383 (t80) REVERT: C 4584 ASP cc_start: 0.6734 (t0) cc_final: 0.6399 (p0) REVERT: C 4644 TRP cc_start: 0.7623 (t60) cc_final: 0.7305 (t-100) REVERT: C 4704 LEU cc_start: 0.8951 (tp) cc_final: 0.8332 (mm) REVERT: C 4726 ASP cc_start: 0.7309 (m-30) cc_final: 0.7056 (m-30) REVERT: C 4887 MET cc_start: 0.8379 (mmm) cc_final: 0.8077 (tpt) REVERT: C 4992 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8416 (mt) REVERT: D 3955 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7075 (mtm) REVERT: D 3959 LYS cc_start: 0.6234 (tttp) cc_final: 0.5950 (tttp) REVERT: D 3986 TRP cc_start: 0.8341 (m100) cc_final: 0.7803 (m100) REVERT: D 4023 MET cc_start: 0.7059 (ttp) cc_final: 0.6673 (ttt) REVERT: D 4042 ARG cc_start: 0.6482 (mtm110) cc_final: 0.5759 (mtm180) REVERT: D 4196 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5857 (tp30) REVERT: D 4199 GLU cc_start: 0.7606 (pm20) cc_final: 0.7133 (tp30) REVERT: D 4209 GLN cc_start: 0.7955 (pt0) cc_final: 0.7442 (pm20) REVERT: D 4212 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: D 4580 TYR cc_start: 0.6886 (t80) cc_final: 0.6385 (t80) REVERT: D 4584 ASP cc_start: 0.6731 (t0) cc_final: 0.6395 (p0) REVERT: D 4644 TRP cc_start: 0.7621 (t60) cc_final: 0.7304 (t-100) REVERT: D 4704 LEU cc_start: 0.8952 (tp) cc_final: 0.8332 (mm) REVERT: D 4726 ASP cc_start: 0.7309 (m-30) cc_final: 0.7059 (m-30) REVERT: D 4887 MET cc_start: 0.8389 (mmm) cc_final: 0.8089 (tpt) REVERT: D 4992 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8410 (mt) outliers start: 55 outliers final: 22 residues processed: 423 average time/residue: 1.2545 time to fit residues: 603.8300 Evaluate side-chains 413 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 376 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3955 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3955 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 92 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 205 optimal weight: 0.0170 chunk 90 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143726 restraints weight = 24646.772| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.93 r_work: 0.3372 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21232 Z= 0.131 Angle : 0.599 17.067 28660 Z= 0.287 Chirality : 0.038 0.196 3096 Planarity : 0.004 0.074 3612 Dihedral : 9.030 149.151 2768 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.81 % Allowed : 17.34 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 2.30 (0.17), residues: 2476 helix: 2.26 (0.12), residues: 1700 sheet: 0.44 (0.68), residues: 64 loop : -0.16 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.003 0.001 HIS B3994 PHE 0.022 0.001 PHE C4922 TYR 0.012 0.001 TYR A4629 ARG 0.013 0.001 ARG B4736 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1388) hydrogen bonds : angle 4.14700 ( 4068) metal coordination : bond 0.00291 ( 16) metal coordination : angle 3.53287 ( 8) SS BOND : bond 0.00054 ( 4) SS BOND : angle 1.46071 ( 8) covalent geometry : bond 0.00291 (21208) covalent geometry : angle 0.59585 (28644) Misc. bond : bond 0.01554 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 383 time to evaluate : 2.426 Fit side-chains REVERT: A 3955 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7046 (mtm) REVERT: A 3959 LYS cc_start: 0.6202 (tttp) cc_final: 0.5879 (tttp) REVERT: A 3986 TRP cc_start: 0.8280 (m100) cc_final: 0.7758 (m100) REVERT: A 3999 MET cc_start: 0.8300 (mmm) cc_final: 0.7883 (tpt) REVERT: A 4023 MET cc_start: 0.6870 (ttp) cc_final: 0.6626 (ttt) REVERT: A 4042 ARG cc_start: 0.6432 (mtm110) cc_final: 0.5707 (mtm180) REVERT: A 4196 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5822 (tp30) REVERT: A 4212 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: A 4580 TYR cc_start: 0.6418 (t80) cc_final: 0.5959 (m-80) REVERT: A 4584 ASP cc_start: 0.6534 (t0) cc_final: 0.6240 (p0) REVERT: A 4644 TRP cc_start: 0.7560 (t60) cc_final: 0.7231 (t-100) REVERT: A 4726 ASP cc_start: 0.7300 (m-30) cc_final: 0.7034 (m-30) REVERT: A 4887 MET cc_start: 0.8388 (mmm) cc_final: 0.8096 (tpt) REVERT: A 4992 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8367 (mt) REVERT: B 3955 MET cc_start: 0.7504 (mmm) cc_final: 0.7272 (mmm) REVERT: B 3959 LYS cc_start: 0.6163 (tttp) cc_final: 0.5854 (tttp) REVERT: B 3986 TRP cc_start: 0.8284 (m100) cc_final: 0.7758 (m100) REVERT: B 3999 MET cc_start: 0.8303 (mmm) cc_final: 0.7889 (tpt) REVERT: B 4023 MET cc_start: 0.6855 (ttp) cc_final: 0.6607 (ttt) REVERT: B 4042 ARG cc_start: 0.6434 (mtm110) cc_final: 0.5707 (mtm180) REVERT: B 4196 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5808 (tp30) REVERT: B 4212 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 4580 TYR cc_start: 0.6423 (t80) cc_final: 0.5963 (m-80) REVERT: B 4584 ASP cc_start: 0.6583 (t0) cc_final: 0.6294 (p0) REVERT: B 4644 TRP cc_start: 0.7560 (t60) cc_final: 0.7231 (t-100) REVERT: B 4726 ASP cc_start: 0.7300 (m-30) cc_final: 0.7031 (m-30) REVERT: B 4887 MET cc_start: 0.8382 (mmm) cc_final: 0.8092 (tpt) REVERT: B 4992 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 3959 LYS cc_start: 0.6182 (tttp) cc_final: 0.5871 (tttp) REVERT: C 3986 TRP cc_start: 0.8287 (m100) cc_final: 0.7766 (m100) REVERT: C 3999 MET cc_start: 0.8302 (mmm) cc_final: 0.7886 (tpt) REVERT: C 4023 MET cc_start: 0.6858 (ttp) cc_final: 0.6611 (ttt) REVERT: C 4042 ARG cc_start: 0.6432 (mtm110) cc_final: 0.5706 (mtm180) REVERT: C 4196 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5812 (tp30) REVERT: C 4212 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: C 4580 TYR cc_start: 0.6423 (t80) cc_final: 0.5960 (m-80) REVERT: C 4584 ASP cc_start: 0.6528 (t0) cc_final: 0.6239 (p0) REVERT: C 4644 TRP cc_start: 0.7556 (t60) cc_final: 0.7226 (t-100) REVERT: C 4726 ASP cc_start: 0.7292 (m-30) cc_final: 0.7025 (m-30) REVERT: C 4887 MET cc_start: 0.8374 (mmm) cc_final: 0.8090 (tpt) REVERT: C 4992 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8373 (mt) REVERT: D 3959 LYS cc_start: 0.6188 (tttp) cc_final: 0.5873 (tttp) REVERT: D 3986 TRP cc_start: 0.8287 (m100) cc_final: 0.7767 (m100) REVERT: D 3999 MET cc_start: 0.8300 (mmm) cc_final: 0.7883 (tpt) REVERT: D 4023 MET cc_start: 0.6865 (ttp) cc_final: 0.6618 (ttt) REVERT: D 4042 ARG cc_start: 0.6435 (mtm110) cc_final: 0.5711 (mtm180) REVERT: D 4196 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5814 (tp30) REVERT: D 4212 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: D 4580 TYR cc_start: 0.6425 (t80) cc_final: 0.5965 (m-80) REVERT: D 4584 ASP cc_start: 0.6523 (t0) cc_final: 0.6230 (p0) REVERT: D 4644 TRP cc_start: 0.7555 (t60) cc_final: 0.7224 (t-100) REVERT: D 4726 ASP cc_start: 0.7301 (m-30) cc_final: 0.7036 (m-30) REVERT: D 4887 MET cc_start: 0.8387 (mmm) cc_final: 0.8102 (tpt) REVERT: D 4992 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8367 (mt) outliers start: 63 outliers final: 22 residues processed: 433 average time/residue: 1.2124 time to fit residues: 599.6864 Evaluate side-chains 416 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 381 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3955 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B3950 ASN B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.176211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142420 restraints weight = 24518.032| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.01 r_work: 0.3376 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21232 Z= 0.145 Angle : 0.661 16.370 28660 Z= 0.319 Chirality : 0.039 0.197 3096 Planarity : 0.004 0.075 3612 Dihedral : 9.092 149.657 2768 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.54 % Allowed : 18.00 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 2.20 (0.17), residues: 2476 helix: 2.22 (0.12), residues: 1704 sheet: 0.33 (0.68), residues: 64 loop : -0.32 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A5019 HIS 0.003 0.001 HIS A3994 PHE 0.024 0.001 PHE C4922 TYR 0.015 0.001 TYR A4580 ARG 0.014 0.001 ARG C4736 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1388) hydrogen bonds : angle 4.26673 ( 4068) metal coordination : bond 0.00468 ( 16) metal coordination : angle 3.60578 ( 8) SS BOND : bond 0.00132 ( 4) SS BOND : angle 1.40874 ( 8) covalent geometry : bond 0.00326 (21208) covalent geometry : angle 0.65763 (28644) Misc. bond : bond 0.01407 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 367 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3986 TRP cc_start: 0.8337 (m100) cc_final: 0.7750 (m100) REVERT: A 3999 MET cc_start: 0.8344 (mmm) cc_final: 0.7928 (tpt) REVERT: A 4023 MET cc_start: 0.6931 (ttp) cc_final: 0.6685 (ttt) REVERT: A 4042 ARG cc_start: 0.6450 (mtm110) cc_final: 0.5732 (mtm180) REVERT: A 4196 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5853 (tp30) REVERT: A 4199 GLU cc_start: 0.7674 (pm20) cc_final: 0.7165 (tp30) REVERT: A 4209 GLN cc_start: 0.7968 (pt0) cc_final: 0.7452 (pm20) REVERT: A 4212 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: A 4644 TRP cc_start: 0.7589 (t60) cc_final: 0.7242 (t-100) REVERT: A 4704 LEU cc_start: 0.8937 (tp) cc_final: 0.8325 (mm) REVERT: A 4726 ASP cc_start: 0.7311 (m-30) cc_final: 0.7032 (m-30) REVERT: A 4887 MET cc_start: 0.8382 (mmm) cc_final: 0.8089 (tpt) REVERT: A 4992 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 3955 MET cc_start: 0.7542 (mmm) cc_final: 0.7298 (mmm) REVERT: B 3986 TRP cc_start: 0.8345 (m100) cc_final: 0.7750 (m100) REVERT: B 3999 MET cc_start: 0.8344 (mmm) cc_final: 0.7945 (tpt) REVERT: B 4023 MET cc_start: 0.6790 (ttp) cc_final: 0.6546 (ttt) REVERT: B 4042 ARG cc_start: 0.6463 (mtm110) cc_final: 0.5741 (mtm180) REVERT: B 4196 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.5860 (tp30) REVERT: B 4199 GLU cc_start: 0.7679 (pm20) cc_final: 0.7165 (tp30) REVERT: B 4209 GLN cc_start: 0.7983 (pt0) cc_final: 0.7461 (pm20) REVERT: B 4212 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: B 4644 TRP cc_start: 0.7575 (t60) cc_final: 0.7228 (t-100) REVERT: B 4704 LEU cc_start: 0.8942 (tp) cc_final: 0.8329 (mm) REVERT: B 4726 ASP cc_start: 0.7314 (m-30) cc_final: 0.7033 (m-30) REVERT: B 4887 MET cc_start: 0.8375 (mmm) cc_final: 0.8082 (tpt) REVERT: B 4992 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8417 (mt) REVERT: C 3986 TRP cc_start: 0.8339 (m100) cc_final: 0.7754 (m100) REVERT: C 3999 MET cc_start: 0.8338 (mmm) cc_final: 0.7919 (tpt) REVERT: C 4023 MET cc_start: 0.6936 (ttp) cc_final: 0.6691 (ttt) REVERT: C 4042 ARG cc_start: 0.6466 (mtm110) cc_final: 0.5744 (mtm180) REVERT: C 4196 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5861 (tp30) REVERT: C 4199 GLU cc_start: 0.7682 (pm20) cc_final: 0.7171 (tp30) REVERT: C 4209 GLN cc_start: 0.7975 (pt0) cc_final: 0.7443 (pm20) REVERT: C 4212 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: C 4644 TRP cc_start: 0.7578 (t60) cc_final: 0.7231 (t-100) REVERT: C 4704 LEU cc_start: 0.8939 (tp) cc_final: 0.8327 (mm) REVERT: C 4726 ASP cc_start: 0.7314 (m-30) cc_final: 0.7029 (m-30) REVERT: C 4887 MET cc_start: 0.8379 (mmm) cc_final: 0.8095 (tpt) REVERT: C 4911 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7613 (mm) REVERT: C 4992 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8407 (mt) REVERT: D 3986 TRP cc_start: 0.8336 (m100) cc_final: 0.7758 (m100) REVERT: D 3999 MET cc_start: 0.8345 (mmm) cc_final: 0.7925 (tpt) REVERT: D 4023 MET cc_start: 0.6914 (ttp) cc_final: 0.6677 (ttt) REVERT: D 4042 ARG cc_start: 0.6462 (mtm110) cc_final: 0.5742 (mtm180) REVERT: D 4196 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5856 (tp30) REVERT: D 4199 GLU cc_start: 0.7665 (pm20) cc_final: 0.7166 (tp30) REVERT: D 4209 GLN cc_start: 0.7965 (pt0) cc_final: 0.7436 (pm20) REVERT: D 4212 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: D 4644 TRP cc_start: 0.7578 (t60) cc_final: 0.7230 (t-100) REVERT: D 4704 LEU cc_start: 0.8942 (tp) cc_final: 0.8332 (mm) REVERT: D 4726 ASP cc_start: 0.7316 (m-30) cc_final: 0.7034 (m-30) REVERT: D 4887 MET cc_start: 0.8376 (mmm) cc_final: 0.8087 (tpt) REVERT: D 4992 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8423 (mt) outliers start: 57 outliers final: 26 residues processed: 409 average time/residue: 1.3300 time to fit residues: 618.2129 Evaluate side-chains 391 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 352 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4878 ASP Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4878 ASP Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4878 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4878 ASP Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 47 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 154 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143244 restraints weight = 24630.036| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.00 r_work: 0.3380 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21232 Z= 0.132 Angle : 0.636 14.261 28660 Z= 0.307 Chirality : 0.038 0.220 3096 Planarity : 0.004 0.074 3612 Dihedral : 9.050 149.996 2768 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.74 % Favored : 98.10 % Rotamer: Outliers : 2.05 % Allowed : 18.18 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 2.20 (0.17), residues: 2476 helix: 2.23 (0.12), residues: 1704 sheet: 0.25 (0.69), residues: 64 loop : -0.33 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5019 HIS 0.003 0.001 HIS D3994 PHE 0.023 0.001 PHE C4922 TYR 0.016 0.001 TYR B4687 ARG 0.014 0.001 ARG D4189 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1388) hydrogen bonds : angle 4.23805 ( 4068) metal coordination : bond 0.00335 ( 16) metal coordination : angle 3.51667 ( 8) SS BOND : bond 0.00032 ( 4) SS BOND : angle 1.35521 ( 8) covalent geometry : bond 0.00295 (21208) covalent geometry : angle 0.63259 (28644) Misc. bond : bond 0.01318 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 367 time to evaluate : 2.447 Fit side-chains REVERT: A 3986 TRP cc_start: 0.8330 (m100) cc_final: 0.7756 (m100) REVERT: A 3999 MET cc_start: 0.8252 (mmm) cc_final: 0.7833 (tpt) REVERT: A 4023 MET cc_start: 0.6746 (ttp) cc_final: 0.6524 (ttt) REVERT: A 4042 ARG cc_start: 0.6422 (mtm110) cc_final: 0.5694 (mtm180) REVERT: A 4184 MET cc_start: 0.8116 (tpp) cc_final: 0.7892 (ttp) REVERT: A 4196 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5810 (tp30) REVERT: A 4199 GLU cc_start: 0.7822 (pm20) cc_final: 0.7285 (tp30) REVERT: A 4212 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 4644 TRP cc_start: 0.7568 (t60) cc_final: 0.7216 (t-100) REVERT: A 4686 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7539 (tm) REVERT: A 4704 LEU cc_start: 0.8932 (tp) cc_final: 0.8317 (mm) REVERT: A 4726 ASP cc_start: 0.7339 (m-30) cc_final: 0.7057 (m-30) REVERT: A 4743 MET cc_start: 0.7162 (ptm) cc_final: 0.6894 (ptm) REVERT: A 4887 MET cc_start: 0.8265 (mmm) cc_final: 0.8004 (tpt) REVERT: A 4992 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 3986 TRP cc_start: 0.8324 (m100) cc_final: 0.7742 (m100) REVERT: B 3999 MET cc_start: 0.8347 (mmm) cc_final: 0.7954 (tpt) REVERT: B 4023 MET cc_start: 0.6750 (ttp) cc_final: 0.6518 (ttt) REVERT: B 4042 ARG cc_start: 0.6434 (mtm110) cc_final: 0.5705 (mtm180) REVERT: B 4184 MET cc_start: 0.8133 (tpp) cc_final: 0.7912 (ttp) REVERT: B 4196 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5816 (tp30) REVERT: B 4199 GLU cc_start: 0.7817 (pm20) cc_final: 0.7294 (tp30) REVERT: B 4212 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: B 4644 TRP cc_start: 0.7565 (t60) cc_final: 0.7209 (t-100) REVERT: B 4686 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7527 (tm) REVERT: B 4704 LEU cc_start: 0.8931 (tp) cc_final: 0.8318 (mm) REVERT: B 4726 ASP cc_start: 0.7338 (m-30) cc_final: 0.7059 (m-30) REVERT: B 4743 MET cc_start: 0.7164 (ptm) cc_final: 0.6902 (ptm) REVERT: B 4887 MET cc_start: 0.8254 (mmm) cc_final: 0.7994 (tpt) REVERT: B 4992 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8394 (mt) REVERT: C 3986 TRP cc_start: 0.8325 (m100) cc_final: 0.7753 (m100) REVERT: C 3999 MET cc_start: 0.8333 (mmm) cc_final: 0.7934 (tpt) REVERT: C 4023 MET cc_start: 0.6755 (ttp) cc_final: 0.6534 (ttt) REVERT: C 4042 ARG cc_start: 0.6423 (mtm110) cc_final: 0.5694 (mtm180) REVERT: C 4184 MET cc_start: 0.8130 (tpp) cc_final: 0.7909 (ttp) REVERT: C 4196 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5815 (tp30) REVERT: C 4199 GLU cc_start: 0.7810 (pm20) cc_final: 0.7289 (tp30) REVERT: C 4212 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: C 4644 TRP cc_start: 0.7557 (t60) cc_final: 0.7208 (t-100) REVERT: C 4686 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7546 (tm) REVERT: C 4704 LEU cc_start: 0.8929 (tp) cc_final: 0.8316 (mm) REVERT: C 4726 ASP cc_start: 0.7340 (m-30) cc_final: 0.7059 (m-30) REVERT: C 4743 MET cc_start: 0.7168 (ptm) cc_final: 0.6903 (ptm) REVERT: C 4887 MET cc_start: 0.8265 (mmm) cc_final: 0.8014 (tpt) REVERT: C 4911 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7590 (mm) REVERT: C 4992 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8389 (mt) REVERT: D 3986 TRP cc_start: 0.8322 (m100) cc_final: 0.7754 (m100) REVERT: D 3999 MET cc_start: 0.8333 (mmm) cc_final: 0.7934 (tpt) REVERT: D 4023 MET cc_start: 0.6742 (ttp) cc_final: 0.6526 (ttt) REVERT: D 4042 ARG cc_start: 0.6428 (mtm110) cc_final: 0.5698 (mtm180) REVERT: D 4184 MET cc_start: 0.8106 (tpp) cc_final: 0.7876 (ttp) REVERT: D 4196 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5815 (tp30) REVERT: D 4199 GLU cc_start: 0.7813 (pm20) cc_final: 0.7289 (tp30) REVERT: D 4212 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: D 4644 TRP cc_start: 0.7557 (t60) cc_final: 0.7206 (t-100) REVERT: D 4686 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7534 (tm) REVERT: D 4704 LEU cc_start: 0.8932 (tp) cc_final: 0.8323 (mm) REVERT: D 4726 ASP cc_start: 0.7342 (m-30) cc_final: 0.7061 (m-30) REVERT: D 4743 MET cc_start: 0.7165 (ptm) cc_final: 0.6901 (ptm) REVERT: D 4887 MET cc_start: 0.8258 (mmm) cc_final: 0.8004 (tpt) REVERT: D 4992 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8391 (mt) outliers start: 46 outliers final: 24 residues processed: 404 average time/residue: 1.2679 time to fit residues: 583.7960 Evaluate side-chains 395 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4686 LEU Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4686 LEU Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4686 LEU Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4686 LEU Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 142 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 208 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN B4034 ASN C4034 ASN D4034 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.178463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144664 restraints weight = 24683.399| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.02 r_work: 0.3385 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21232 Z= 0.133 Angle : 0.699 23.733 28660 Z= 0.326 Chirality : 0.038 0.203 3096 Planarity : 0.004 0.072 3612 Dihedral : 9.052 150.003 2768 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.14 % Allowed : 18.23 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 2.17 (0.17), residues: 2476 helix: 2.23 (0.12), residues: 1700 sheet: 0.28 (0.69), residues: 64 loop : -0.40 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B5019 HIS 0.003 0.001 HIS C3994 PHE 0.026 0.001 PHE A4922 TYR 0.019 0.001 TYR B4687 ARG 0.015 0.001 ARG C4736 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 1388) hydrogen bonds : angle 4.27606 ( 4068) metal coordination : bond 0.00205 ( 16) metal coordination : angle 3.45564 ( 8) SS BOND : bond 0.00059 ( 4) SS BOND : angle 1.56486 ( 8) covalent geometry : bond 0.00293 (21208) covalent geometry : angle 0.69619 (28644) Misc. bond : bond 0.01463 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 368 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3986 TRP cc_start: 0.8289 (m100) cc_final: 0.7756 (m100) REVERT: A 3999 MET cc_start: 0.8259 (mmm) cc_final: 0.7849 (tpt) REVERT: A 4042 ARG cc_start: 0.6443 (mtm110) cc_final: 0.5708 (mtm180) REVERT: A 4184 MET cc_start: 0.8078 (tpp) cc_final: 0.7859 (ttp) REVERT: A 4196 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5940 (tp30) REVERT: A 4199 GLU cc_start: 0.7814 (pm20) cc_final: 0.7294 (tp30) REVERT: A 4212 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: A 4644 TRP cc_start: 0.7613 (t60) cc_final: 0.7266 (t-100) REVERT: A 4686 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7172 (tp) REVERT: A 4704 LEU cc_start: 0.8924 (tp) cc_final: 0.8307 (mm) REVERT: A 4726 ASP cc_start: 0.7394 (m-30) cc_final: 0.7161 (m-30) REVERT: A 4736 ARG cc_start: 0.6964 (ttp-110) cc_final: 0.6566 (ttp-110) REVERT: A 4743 MET cc_start: 0.7171 (ptm) cc_final: 0.6909 (ptm) REVERT: A 4887 MET cc_start: 0.8275 (mmm) cc_final: 0.8006 (tpt) REVERT: A 4992 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8375 (mt) REVERT: B 3986 TRP cc_start: 0.8282 (m100) cc_final: 0.7746 (m100) REVERT: B 3999 MET cc_start: 0.8341 (mmm) cc_final: 0.7956 (tpt) REVERT: B 4023 MET cc_start: 0.6718 (ttp) cc_final: 0.6489 (ttt) REVERT: B 4042 ARG cc_start: 0.6388 (mtm110) cc_final: 0.5659 (mtm180) REVERT: B 4184 MET cc_start: 0.8085 (tpp) cc_final: 0.7866 (ttp) REVERT: B 4196 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5937 (tp30) REVERT: B 4199 GLU cc_start: 0.7805 (pm20) cc_final: 0.7290 (tp30) REVERT: B 4212 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: B 4644 TRP cc_start: 0.7611 (t60) cc_final: 0.7265 (t-100) REVERT: B 4686 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7165 (tp) REVERT: B 4704 LEU cc_start: 0.8920 (tp) cc_final: 0.8301 (mm) REVERT: B 4726 ASP cc_start: 0.7388 (m-30) cc_final: 0.7155 (m-30) REVERT: B 4736 ARG cc_start: 0.6960 (ttp-110) cc_final: 0.6560 (ttp-110) REVERT: B 4743 MET cc_start: 0.7169 (ptm) cc_final: 0.6905 (ptm) REVERT: B 4887 MET cc_start: 0.8270 (mmm) cc_final: 0.7997 (tpt) REVERT: B 4992 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 3986 TRP cc_start: 0.8289 (m100) cc_final: 0.7760 (m100) REVERT: C 3999 MET cc_start: 0.8311 (mmm) cc_final: 0.7910 (tpt) REVERT: C 4042 ARG cc_start: 0.6386 (mtm110) cc_final: 0.5658 (mtm180) REVERT: C 4184 MET cc_start: 0.8085 (tpp) cc_final: 0.7865 (ttp) REVERT: C 4196 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5940 (tp30) REVERT: C 4199 GLU cc_start: 0.7808 (pm20) cc_final: 0.7293 (tp30) REVERT: C 4212 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: C 4644 TRP cc_start: 0.7608 (t60) cc_final: 0.7246 (t-100) REVERT: C 4686 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7183 (tp) REVERT: C 4704 LEU cc_start: 0.8922 (tp) cc_final: 0.8307 (mm) REVERT: C 4726 ASP cc_start: 0.7396 (m-30) cc_final: 0.7164 (m-30) REVERT: C 4736 ARG cc_start: 0.6958 (ttp-110) cc_final: 0.6559 (ttp-110) REVERT: C 4743 MET cc_start: 0.7172 (ptm) cc_final: 0.6910 (ptm) REVERT: C 4887 MET cc_start: 0.8278 (mmm) cc_final: 0.8016 (tpt) REVERT: C 4911 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7579 (mm) REVERT: C 4992 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8373 (mt) REVERT: D 3986 TRP cc_start: 0.8291 (m100) cc_final: 0.7764 (m100) REVERT: D 3999 MET cc_start: 0.8306 (mmm) cc_final: 0.7906 (tpt) REVERT: D 4042 ARG cc_start: 0.6394 (mtm110) cc_final: 0.5666 (mtm180) REVERT: D 4184 MET cc_start: 0.8069 (tpp) cc_final: 0.7843 (ttp) REVERT: D 4196 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5946 (tp30) REVERT: D 4199 GLU cc_start: 0.7809 (pm20) cc_final: 0.7299 (tp30) REVERT: D 4212 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: D 4644 TRP cc_start: 0.7603 (t60) cc_final: 0.7257 (t-100) REVERT: D 4686 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7176 (tp) REVERT: D 4704 LEU cc_start: 0.8924 (tp) cc_final: 0.8308 (mm) REVERT: D 4726 ASP cc_start: 0.7387 (m-30) cc_final: 0.7154 (m-30) REVERT: D 4736 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6557 (ttp-110) REVERT: D 4743 MET cc_start: 0.7172 (ptm) cc_final: 0.6912 (ptm) REVERT: D 4887 MET cc_start: 0.8277 (mmm) cc_final: 0.8010 (tpt) REVERT: D 4992 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8372 (mt) outliers start: 48 outliers final: 27 residues processed: 407 average time/residue: 1.3169 time to fit residues: 612.2494 Evaluate side-chains 396 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 352 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4686 LEU Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4878 ASP Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4686 LEU Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4878 ASP Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4686 LEU Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4878 ASP Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4686 LEU Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4878 ASP Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 245 optimal weight: 0.0970 chunk 171 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN B4034 ASN C4034 ASN D4034 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.178378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144731 restraints weight = 24932.326| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.00 r_work: 0.3404 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21232 Z= 0.129 Angle : 0.697 22.610 28660 Z= 0.326 Chirality : 0.039 0.244 3096 Planarity : 0.004 0.070 3612 Dihedral : 9.014 149.896 2768 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.58 % Favored : 98.26 % Rotamer: Outliers : 2.05 % Allowed : 18.54 % Favored : 79.41 % 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: 2.10 (0.17), residues: 2476 helix: 2.20 (0.12), residues: 1700 sheet: 0.30 (0.70), residues: 64 loop : -0.48 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B4644 HIS 0.003 0.001 HIS B3994 PHE 0.027 0.001 PHE A4922 TYR 0.015 0.001 TYR D4687 ARG 0.016 0.001 ARG A4189 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1388) hydrogen bonds : angle 4.25442 ( 4068) metal coordination : bond 0.00290 ( 16) metal coordination : angle 4.04049 ( 8) SS BOND : bond 0.00036 ( 4) SS BOND : angle 1.49807 ( 8) covalent geometry : bond 0.00282 (21208) covalent geometry : angle 0.69328 (28644) Misc. bond : bond 0.01441 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18252.99 seconds wall clock time: 312 minutes 18.44 seconds (18738.44 seconds total)